Switch to version 3.0.0b37

taxon name.

MANIFEST.in

@@ -6,7 +6,7 @@ recursive-include doc/sphinx/source *.txt *.rst *.py
 recursive-include doc/sphinx/sphinxext *.py
 include doc/sphinx/Makefile
 include doc/sphinx/Doxyfile
-include README.txt
+include README.md
 include requirements.txt
 include scripts/obi
 

obi_completion_script.bash

@@ -1,4 +1,3 @@
-#/usr/bin/env bash
 
 _obi_comp ()
 {

python/obitools3/apps/optiongroups/__init__.py

@@ -39,6 +39,12 @@ def __addImportInputOption(optionManager):
                      const=b'fastq',
                      help="Input file is in fastq format")
 
+    group.add_argument('--silva-input',
+                     action="store_const", dest="obi:inputformat",
+                     default=None,
+                     const=b'silva',
+                     help="Input file is in SILVA fasta format")
+
     group.add_argument('--embl-input',
                      action="store_const", dest="obi:inputformat",
                      default=None,
@@ -55,7 +61,7 @@ def __addImportInputOption(optionManager):
                      action="store_const", dest="obi:inputformat",
                      default=None,
                      const=b'ngsfilter',
-                     help="Input file is an ngsfilter file")
+                     help="Input file is an ngsfilter file. If not using tags, use ':' or 'None:None' or '-:-' or any combination")
 
     group.add_argument('--ecopcr-result-input',
                      action="store_const", dest="obi:inputformat",
@@ -222,7 +228,7 @@ def __addDMSOutputOption(optionManager):
     group.add_argument('--no-create-dms',
                  action="store_true", dest="obi:nocreatedms",
                  default=False,
-                 help="Don't create an output DMS it does not already exist")
+                 help="Don't create an output DMS if it does not already exist")
 
 
 def __addEltLimitOption(optionManager):

python/obitools3/apps/progress.pyx

@@ -30,12 +30,12 @@ cdef class ProgressBar:
                  off_t maxi,
                  dict  config={},
                  str head="",
-                 double seconde=0.1,
+                 double seconds=5,
                  cut=False):
         
         self.starttime = self.clock()
         self.lasttime  = self.starttime
-        self.tickcount = <clock_t> (seconde * CLOCKS_PER_SEC)
+        self.tickcount = <clock_t> (seconds * CLOCKS_PER_SEC)
         self.freq      = 1
         self.cycle     = 0
         self.arrow     = 0

python/obitools3/commands/addtaxids.pyx

@@ -0,0 +1,230 @@
+#cython: language_level=3
+
+from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
+from obitools3.dms import DMS
+from obitools3.dms.view.view cimport View, Line_selection
+from obitools3.uri.decode import open_uri
+from obitools3.apps.optiongroups import addMinimalInputOption, addTaxonomyOption, addMinimalOutputOption, addNoProgressBarOption
+from obitools3.dms.view import RollbackException
+from obitools3.dms.column.column cimport Column
+from functools import reduce
+from obitools3.apps.config import logger
+from obitools3.utils cimport tobytes, str2bytes, tostr
+from io import BufferedWriter
+from obitools3.dms.capi.obiview cimport NUC_SEQUENCE_COLUMN, \
+                                        ID_COLUMN, \
+                                        DEFINITION_COLUMN, \
+                                        QUALITY_COLUMN, \
+                                        COUNT_COLUMN, \
+                                        TAXID_COLUMN
+from obitools3.dms.capi.obitypes cimport OBI_INT
+from obitools3.dms.capi.obitaxonomy cimport MIN_LOCAL_TAXID
+import time
+import math 
+import sys
+
+from cpython.exc cimport PyErr_CheckSignals
+
+ 
+__title__="Annotate sequences with their corresponding NCBI taxid found from the taxon scientific name."
+
+
+ 
+def addOptions(parser):
+    
+    addMinimalInputOption(parser)
+    addTaxonomyOption(parser)
+    addMinimalOutputOption(parser)
+    addNoProgressBarOption(parser)
+
+    group=parser.add_argument_group('obi addtaxids specific options')
+
+    group.add_argument('-t', '--taxid-tag', 
+                       action="store", 
+                       dest="addtaxids:taxid_tag",
+                       metavar="<TAXID_TAG>",
+                       default=b"TAXID",
+                       help="Name of the tag to store the found taxid "
+                            "(default: 'TAXID'.")
+
+    group.add_argument('-n', '--taxon-name-tag', 
+                       action="store", 
+                       dest="addtaxids:taxon_name_tag",
+                       metavar="<SCIENTIFIC_NAME_TAG>",
+                       default=b"SCIENTIFIC_NAME",
+                       help="Name of the tag giving the scientific name of the taxon "
+                            "(default: 'SCIENTIFIC_NAME'.")
+
+    group.add_argument('-g', '--try-genus-match',
+                     action="store_true", dest="addtaxids:try_genus_match",
+                     default=False,
+                     help="Try matching the first word of <SCIENTIFIC_NAME_TAG> when can't find corresponding taxid for a taxon. "
+                          "If there is a match it is added in the 'parent_taxid' tag. (Can be used by 'obi taxonomy' to add the taxon under that taxid).")
+
+    group.add_argument('-a', '--restricting-ancestor', 
+                       action="store", 
+                       dest="addtaxids:restricting_ancestor",
+                       metavar="<RESTRICTING_ANCESTOR>",
+                       default=None,
+                       help="Enables to restrict the search of taxids under an ancestor specified by its taxid.")
+
+    group.add_argument('-l', '--log-file', 
+                       action="store", 
+                       dest="addtaxids:log_file",
+                       metavar="<LOG_FILE>",
+                       default='',
+                       help="Path to a log file to write informations about not found taxids.")
+
+
+def run(config):
+     
+    DMS.obi_atexit()
+    
+    logger("info", "obi addtaxids")
+
+    # Open the input
+    input = open_uri(config['obi']['inputURI'])
+    if input is None:
+        raise Exception("Could not read input view")
+    i_dms = input[0]
+    i_view = input[1]
+    i_view_name = input[1].name
+
+    # Open the output: only the DMS, as the output view is going to be created by cloning the input view
+    # (could eventually be done via an open_uri() argument)
+    output = open_uri(config['obi']['outputURI'],
+                      input=False,
+                      dms_only=True)
+    if output is None:
+        raise Exception("Could not create output view")
+    o_dms = output[0]
+    output_0 = output[0]
+    o_view_name = output[1]
+
+    # stdout output: create temporary view
+    if type(output_0)==BufferedWriter:
+        o_dms = i_dms
+        i=0
+        o_view_name = b"temp"
+        while o_view_name in i_dms: # Making sure view name is unique in output DMS
+            o_view_name = o_view_name+b"_"+str2bytes(str(i))
+            i+=1
+        imported_view_name = o_view_name
+
+    # If the input and output DMS are not the same, import the input view in the output DMS before cloning it to modify it
+    # (could be the other way around: clone and modify in the input DMS then import the new view in the output DMS)
+    if i_dms != o_dms:
+        imported_view_name = i_view_name
+        i=0
+        while imported_view_name in o_dms:  # Making sure view name is unique in output DMS
+            imported_view_name = i_view_name+b"_"+str2bytes(str(i))
+            i+=1
+        View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], i_view_name, imported_view_name)
+        i_view = o_dms[imported_view_name]
+
+    # Clone output view from input view
+    o_view = i_view.clone(o_view_name)
+    if o_view is None:
+        raise Exception("Couldn't create output view")
+    i_view.close()
+
+    # Open taxonomy
+    taxo_uri = open_uri(config['obi']['taxoURI'])
+    if taxo_uri is None or taxo_uri[2] == bytes:
+        raise Exception("Couldn't open taxonomy")
+    taxo = taxo_uri[1]
+
+    # Initialize the progress bar
+    if config['obi']['noprogressbar'] == False:
+        pb = ProgressBar(len(o_view), config)
+    else:
+        pb = None
+        
+    try:
+        if config['addtaxids']['log_file']:
+            logfile = open(config['addtaxids']['log_file'], 'w')
+        else:
+            logfile = None
+        if config['addtaxids']['try_genus_match']:
+            try_genus = True
+        else:
+            try_genus = False
+        if 'restricting_ancestor' in config['addtaxids']:
+            res_anc = int(config['addtaxids']['restricting_ancestor'])
+        else:
+            res_anc = None
+        taxid_column_name = config['addtaxids']['taxid_tag']
+        parent_taxid_column_name = "PARENT_TAXID" # TODO macro
+        taxon_name_column_name = config['addtaxids']['taxon_name_tag']
+        taxid_column = Column.new_column(o_view, taxid_column_name, OBI_INT)
+        parent_taxid_column = Column.new_column(o_view, parent_taxid_column_name, OBI_INT)
+        taxon_name_column = o_view[taxon_name_column_name]
+        
+        found_count = 0
+        not_found_count = 0
+        parent_found_count = 0
+        
+        for i in range(len(o_view)):
+            PyErr_CheckSignals()
+            if pb is not None:
+                pb(i)
+            taxon_name = taxon_name_column[i]
+            taxon = taxo.get_taxon_by_name(taxon_name, res_anc)
+            if taxon is not None:
+                taxid_column[i] = taxon.taxid
+                found_count+=1
+            elif try_genus: # try finding genus or other parent taxon from the first word
+                taxon_name_sp = taxon_name.split(b" ")
+                taxon = taxo.get_taxon_by_name(taxon_name_sp[0], res_anc)
+                if taxon is not None:
+                    parent_taxid_column[i] = taxon.taxid
+                    parent_found_count+=1
+                    if logfile:
+                        print("Found parent taxon for", tostr(taxon_name), file=logfile)
+                else:
+                    not_found_count+=1
+                    if logfile:
+                        print("No taxid found for", tostr(taxon_name), file=logfile)
+            else:
+                not_found_count+=1
+                if logfile:
+                    print("No taxid found for", tostr(taxon_name), file=logfile)
+
+    except Exception, e:
+        raise RollbackException("obi addtaxids error, rollbacking view: "+str(e), o_view)
+
+    if pb is not None:
+        pb(i, force=True)
+        print("", file=sys.stderr)
+    
+    logger("info", "\nTaxids found: "+str(found_count)+"/"+str(len(o_view))+" ("+str(round(found_count*100.0/len(o_view), 2))+"%)")
+    if config['addtaxids']['try_genus_match']:
+        logger("info", "\nParent taxids found: "+str(parent_found_count)+"/"+str(len(o_view))+" ("+str(round(parent_found_count*100.0/len(o_view), 2))+"%)")
+    logger("info", "\nTaxids not found: "+str(not_found_count)+"/"+str(len(o_view))+" ("+str(round(not_found_count*100.0/len(o_view), 2))+"%)") 
+    
+    # Save command config in View and DMS comments
+    command_line = " ".join(sys.argv[1:])
+    input_dms_name=[input[0].name]
+    input_view_name=[i_view_name]
+    if 'taxoURI' in config['obi'] and config['obi']['taxoURI'] is not None:
+        input_dms_name.append(config['obi']['taxoURI'].split("/")[-3])
+        input_view_name.append("taxonomy/"+config['obi']['taxoURI'].split("/")[-1])
+    o_view.write_config(config, "addtaxids", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
+    o_dms.record_command_line(command_line)
+
+    #print("\n\nOutput view:\n````````````", file=sys.stderr)
+    #print(repr(o_view), file=sys.stderr)
+
+    # stdout output: write to buffer
+    if type(output_0)==BufferedWriter:
+        logger("info", "Printing to output...")
+        o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
+        o_view.close()
+
+    # If the input and the output DMS are different or if stdout output, delete the temporary imported view used to create the final view
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
+        View.delete_view(o_dms, imported_view_name)
+        o_dms.close(force=True)
+    i_dms.close(force=True)
+
+    logger("info", "Done.")

python/obitools3/commands/align.pyx

@@ -4,7 +4,7 @@ from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
 from obitools3.dms import DMS
 from obitools3.dms.view.view cimport View
 from obitools3.uri.decode import open_uri
-from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption
+from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption, addNoProgressBarOption
 from obitools3.dms.view import RollbackException
 from obitools3.apps.config import logger
 from obitools3.utils cimport tobytes, str2bytes
@@ -12,6 +12,9 @@ from obitools3.utils cimport tobytes, str2bytes
 from obitools3.dms.capi.obilcsalign cimport obi_lcs_align_one_column, \
                                             obi_lcs_align_two_columns
 
+from io import BufferedWriter
+from cpython.exc cimport PyErr_CheckSignals
+
 import time
 import sys
 
@@ -23,6 +26,7 @@ def addOptions(parser):
    
    addMinimalInputOption(parser)
    addMinimalOutputOption(parser)
+   addNoProgressBarOption(parser)
 
    group=parser.add_argument_group('obi align specific options')
 
@@ -201,20 +205,20 @@ def run(config):
     if output is None:
         raise Exception("Could not create output")
     o_dms = output[0]
+    output_0 = output[0]
     o_dms_name = o_dms.name 
     final_o_view_name = output[1]
+    o_view_name = final_o_view_name
 
-    # If the input and output DMS are not the same, align creating a temporary view in the input dms that will be exported to 
+    # If stdout output or the input and output DMS are not the same, align creating a temporary view in the input dms that will be exported to 
     # the right DMS and deleted in the other afterwards.
-    if i_dms != o_dms:
-        temporary_view_name = final_o_view_name
-        i=0
-        while temporary_view_name in i_dms:  # Making sure view name is unique in input DMS
-            temporary_view_name = final_o_view_name+b"_"+str2bytes(str(i))
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
+        if type(output_0)==BufferedWriter:
+            o_dms = i_dms
+        o_view_name = b"temp"
+        while o_view_name in i_dms:   # Making sure view name is unique in input DMS
+            o_view_name = o_view_name+b"_"+str2bytes(str(i))
             i+=1
-        o_view_name = temporary_view_name
-    else:
-        o_view_name = final_o_view_name
         
     # Save command config in View comments
     command_line = " ".join(sys.argv[1:])
@@ -263,12 +267,19 @@ def run(config):
         View.delete_view(i_dms, i_view_name_2)
         i_dms_2.close()
 
+    # stdout output: write to buffer
+    if type(output_0)==BufferedWriter:
+        logger("info", "Printing to output...")
+        o_view = o_dms[o_view_name]
+        o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
+        o_view.close()
+
     # If the input and the output DMS are different, delete the temporary result view in the input DMS
-    if i_dms != o_dms:
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
         View.delete_view(i_dms, o_view_name)
-        o_dms.close()
+        o_dms.close(force=True)
     
-    i_dms.close()
+    i_dms.close(force=True)
     
     logger("info", "Done.")
   

python/obitools3/commands/alignpairedend.pyx

@@ -6,7 +6,7 @@ from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
 from obitools3.dms.column.column cimport Column
 from obitools3.dms.capi.obiview cimport QUALITY_COLUMN
 from obitools3.dms.capi.obitypes cimport OBI_QUAL
-from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption
+from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption, addNoProgressBarOption
 from obitools3.uri.decode import open_uri
 from obitools3.apps.config import logger
 from obitools3.libalign._qsassemble import QSolexaReverseAssemble
@@ -14,8 +14,10 @@ from obitools3.libalign._qsrassemble import QSolexaRightReverseAssemble
 from obitools3.libalign._solexapairend import buildConsensus, buildJoinedSequence
 from obitools3.dms.obiseq cimport Nuc_Seq
 from obitools3.libalign.shifted_ali cimport Kmer_similarity, Ali_shifted
-from obitools3.commands.ngsfilter import REVERSE_SEQ_COLUMN_NAME, REVERSE_QUALITY_COLUMN_NAME
+from obitools3.dms.capi.obiview cimport REVERSE_SEQUENCE_COLUMN, REVERSE_QUALITY_COLUMN
+from obitools3.utils cimport str2bytes
 
+from io import BufferedWriter
 import sys
 import os
 
@@ -29,6 +31,7 @@ def addOptions(parser):
 
     addMinimalInputOption(parser)
     addMinimalOutputOption(parser)
+    addNoProgressBarOption(parser)
  
     group = parser.add_argument_group('obi alignpairedend specific options')
 
@@ -39,12 +42,13 @@ def addOptions(parser):
                      type=str,
                      help="URI to the reverse reads if they are in a different view than the forward reads")
 
-    group.add_argument('--score-min',
-                     action="store", dest="alignpairedend:smin",
-                     metavar="#.###",
-                     default=None,
-                     type=float,
-                     help="Minimum score for keeping alignments")
+#     group.add_argument('--score-min',
+#                      action="store", dest="alignpairedend:smin",
+#                      metavar="#.###",
+#                      default=None,
+#                      type=float,
+#                      help="Minimum score for keeping alignments. " 
+#                           "(for kmer alignment) The score is an approximation of the number of nucleotides matching in the overlap of the alignment.")
 
 #     group.add_argument('-A', '--true-ali',
 #                        action="store_true", dest="alignpairedend:trueali",
@@ -102,7 +106,7 @@ def alignmentIterator(entries, aligner):
             seqR = reverse[i]
         else:
             seqF = Nuc_Seq.new_from_stored(entries[i])
-            seqR = Nuc_Seq(seqF.id, seqF[REVERSE_SEQ_COLUMN_NAME], quality=seqF[REVERSE_QUALITY_COLUMN_NAME])
+            seqR = Nuc_Seq(seqF.id, seqF[REVERSE_SEQUENCE_COLUMN], quality=seqF[REVERSE_QUALITY_COLUMN])
             seqR.index = i
         
         ali = aligner(seqF, seqR)
@@ -170,18 +174,29 @@ def run(config):
     if output is None:
         raise Exception("Could not create output view")
 
-    view = output[1]
+    output_0 = output[0]
+    o_dms = output[0]
     
-    Column.new_column(view, QUALITY_COLUMN, OBI_QUAL)   #TODO output URI quality option?
-
-    if 'smin' in config['alignpairedend']:
-        smin = config['alignpairedend']['smin']
+    # stdout output: create temporary view
+    if type(output_0)==BufferedWriter:
+        i_dms = forward.dms   # using any dms
+        o_dms = i_dms
+        i=0
+        o_view_name = b"temp"
+        while o_view_name in i_dms:   # Making sure view name is unique in input DMS
+            o_view_name = o_view_name+b"_"+str2bytes(str(i))
+            i+=1
+        o_view = View_NUC_SEQS.new(o_dms, o_view_name, quality=True)
     else:
-        smin = 0
+        o_view = output[1]
+        Column.new_column(o_view, QUALITY_COLUMN, OBI_QUAL)
 
     # Initialize the progress bar
-    pb = ProgressBar(entries_len, config, seconde=5)
-    
+    if config['obi']['noprogressbar'] == False:
+        pb = ProgressBar(entries_len, config)
+    else:
+        pb = None
+         
     #if config['alignpairedend']['trueali']:
     #    kmer_ali = False
     #    aligner = buildAlignment
@@ -196,8 +211,8 @@ def run(config):
                                   reversed_column=None)
     else:
         aligner = Kmer_similarity(entries, \
-                                  column2=entries[REVERSE_SEQ_COLUMN_NAME], \
-                                  qual_column2=entries[REVERSE_QUALITY_COLUMN_NAME], \
+                                  column2=entries[REVERSE_SEQUENCE_COLUMN], \
+                                  qual_column2=entries[REVERSE_QUALITY_COLUMN], \
                                   kmer_size=config['alignpairedend']['kmersize'], \
                                   reversed_column=entries[b'reversed'])  # column created by the ngsfilter tool
         
@@ -206,51 +221,63 @@ def run(config):
     i = 0
     for ali in ba:
         
-        pb(i)
+        if pb is not None:
+            pb(i)
         
         PyErr_CheckSignals()
 
-        consensus = view[i]
+        consensus = o_view[i]
                
         if not two_views:
             seqF = entries[i]
         else:
             seqF = forward[i]
                         
-        if ali.score > smin and ali.consensus_len > 0 :
+        if ali.overlap_len > 0 :
             buildConsensus(ali, consensus, seqF)
         else:
             if not two_views:
-                seqR = Nuc_Seq(seqF.id, seqF[REVERSE_SEQ_COLUMN_NAME], quality = seqF[REVERSE_QUALITY_COLUMN_NAME])
+                seqR = Nuc_Seq(seqF.id, seqF[REVERSE_SEQUENCE_COLUMN], quality = seqF[REVERSE_QUALITY_COLUMN])
             else:
                 seqR = reverse[i]
             buildJoinedSequence(ali, seqR, consensus, forward=seqF)
-        
-        consensus[b"smin"] = smin
-           
+                   
         if kmer_ali :
             ali.free()
     
         i+=1
 
-    pb(i, force=True)
-    print("", file=sys.stderr)
+    if pb is not None:
+        pb(i, force=True)
+        print("", file=sys.stderr)
 
     if kmer_ali :
         aligner.free()
 
     # Save command config in View and DMS comments
     command_line = " ".join(sys.argv[1:])
-    view.write_config(config, "alignpairedend", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
-    output[0].record_command_line(command_line)
+    o_view.write_config(config, "alignpairedend", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
+    o_dms.record_command_line(command_line)
 
     #print("\n\nOutput view:\n````````````", file=sys.stderr)
     #print(repr(view), file=sys.stderr)
-    
-    input[0].close()
+
+    # stdout output: write to buffer
+    if type(output_0)==BufferedWriter:
+        logger("info", "Printing to output...")
+        o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
+        o_view.close()
+
+    # If stdout output, delete the temporary imported view used to create the final file
+    if type(output_0)==BufferedWriter:
+        View_NUC_SEQS.delete_view(o_dms, o_view_name)
+        output_0.close()
+
+    # Close all DMS
+    input[0].close(force=True)
     if two_views:
-        rinput[0].close()
-    output[0].close()
+        rinput[0].close(force=True)
+    o_dms.close(force=True)
 
     logger("info", "Done.")
     

python/obitools3/commands/annotate.pyx

@@ -4,16 +4,18 @@ from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
 from obitools3.dms import DMS
 from obitools3.dms.view.view cimport View, Line_selection
 from obitools3.uri.decode import open_uri
-from obitools3.apps.optiongroups import addMinimalInputOption, addTaxonomyOption, addMinimalOutputOption
+from obitools3.apps.optiongroups import addMinimalInputOption, addTaxonomyOption, addMinimalOutputOption, addNoProgressBarOption
 from obitools3.dms.view import RollbackException
 from functools import reduce
 from obitools3.apps.config import logger
 from obitools3.utils cimport tobytes, str2bytes
+from io import BufferedWriter
 from obitools3.dms.capi.obiview cimport NUC_SEQUENCE_COLUMN, \
                                         ID_COLUMN, \
                                         DEFINITION_COLUMN, \
                                         QUALITY_COLUMN, \
-                                        COUNT_COLUMN
+                                        COUNT_COLUMN, \
+                                        TAXID_COLUMN
 
 import time
 import math 
@@ -33,6 +35,7 @@ def addOptions(parser):
     addMinimalInputOption(parser)
     addTaxonomyOption(parser)
     addMinimalOutputOption(parser)
+    addNoProgressBarOption(parser)
 
     group=parser.add_argument_group('obi annotate specific options')
  
@@ -175,8 +178,8 @@ def sequenceTaggerGenerator(config, taxo=None):
             counter[0]+=1
                             
         for rank in annoteRank:
-            if 'taxid' in seq:
-                taxid = seq['taxid']
+            if TAXID_COLUMN in seq:
+                taxid = seq[TAXID_COLUMN]
                 if taxid is not None:
                     rtaxid = taxo.get_taxon_at_rank(taxid, rank)
                     if rtaxid is not None:
@@ -190,58 +193,50 @@ def sequenceTaggerGenerator(config, taxo=None):
             seq['seq_rank']=counter[0]
     
         for i,v in toSet:
-            #try:
-            if taxo is not None:
-                environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math}
-            else:
-                environ = {'sequence':seq, 'counter':counter[0], 'math':math}
-            val = eval(v, environ, seq)
-            #except Exception,e:       # TODO discuss usefulness of this
-            #    if options.onlyValid:
-            #        raise e
-            #    val = v
+            try:
+                if taxo is not None:
+                    environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math}
+                else:
+                    environ = {'sequence':seq, 'counter':counter[0], 'math':math}
+                val = eval(v, environ, seq)
+            except Exception:       # set string if not a valid expression
+                val = v
             seq[i]=val
 
         if length:
             seq['seq_length']=len(seq)
 
         if newId is not None:
-#            try:
-            if taxo is not None:
-                environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math}
-            else:
-                environ = {'sequence':seq, 'counter':counter[0], 'math':math}     
-            val = eval(newId, environ, seq)
-#            except Exception,e:
-#                if options.onlyValid:
-#                    raise e
-#                val = newId
+            try:
+                if taxo is not None:
+                    environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math}
+                else:
+                    environ = {'sequence':seq, 'counter':counter[0], 'math':math}     
+                val = eval(newId, environ, seq)
+            except Exception:      # set string if not a valid expression
+                val = newId
             seq.id=val
 
         if newDef is not None:
-#            try:
-            if taxo is not None:
-                environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math}
-            else:
-                environ = {'sequence':seq, 'counter':counter[0], 'math':math}     
-            val = eval(newDef, environ, seq)
-#            except Exception,e:
-#                if options.onlyValid:
-#                    raise e
-#                val = newDef
+            try:
+                if taxo is not None:
+                    environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math}
+                else:
+                    environ = {'sequence':seq, 'counter':counter[0], 'math':math}     
+                val = eval(newDef, environ, seq)
+            except Exception:    # set string if not a valid expression
+                val = newDef
             seq.definition=val
-#             
+             
         if newSeq is not None:
-#            try:
-            if taxo is not None:
-                environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math}
-            else:
-                environ = {'sequence':seq, 'counter':counter[0], 'math':math}     
-            val = eval(newSeq, environ, seq)
-#            except Exception,e:
-#                if options.onlyValid:
-#                    raise e
-#                val = newSeq
+            try:
+                if taxo is not None:
+                    environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math}
+                else:
+                    environ = {'sequence':seq, 'counter':counter[0], 'math':math}     
+                val = eval(newSeq, environ, seq)
+            except Exception:    # set string if not a valid expression
+                val = newSeq
             seq.seq=val
             if 'seq_length' in seq:
                 seq['seq_length']=len(seq)
@@ -251,15 +246,14 @@ def sequenceTaggerGenerator(config, taxo=None):
                 seq.view.delete_column(QUALITY_COLUMN)
                     
         if run is not None:
-#            try:
-            if taxo is not None:
-                environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math}
-            else:
-                environ = {'sequence':seq, 'counter':counter[0], 'math':math}     
-            eval(run, environ, seq)
-#            except Exception,e:
-#                if options.onlyValid:
-#                    raise e
+            try:
+                if taxo is not None:
+                    environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math}
+                else:
+                    environ = {'sequence':seq, 'counter':counter[0], 'math':math}     
+                eval(run, environ, seq)
+            except Exception,e:
+                raise e
 
     return sequenceTagger
 
@@ -286,8 +280,19 @@ def run(config):
     if output is None:
         raise Exception("Could not create output view")
     o_dms = output[0]
+    output_0 = output[0]
     o_view_name = output[1]
-    
+
+    # stdout output: create temporary view
+    if type(output_0)==BufferedWriter:
+        o_dms = i_dms
+        i=0
+        o_view_name = b"temp"
+        while o_view_name in i_dms: # Making sure view name is unique in output DMS
+            o_view_name = o_view_name+b"_"+str2bytes(str(i))
+            i+=1
+        imported_view_name = o_view_name
+
     # If the input and output DMS are not the same, import the input view in the output DMS before cloning it to modify it
     # (could be the other way around: clone and modify in the input DMS then import the new view in the output DMS)
     if i_dms != o_dms:
@@ -298,7 +303,7 @@ def run(config):
             i+=1
         View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], i_view_name, imported_view_name)
         i_view = o_dms[imported_view_name]
-        
+
     # Clone output view from input view
     o_view = i_view.clone(o_view_name)
     if o_view is None:
@@ -315,7 +320,10 @@ def run(config):
         taxo = None
 
     # Initialize the progress bar
-    pb = ProgressBar(len(o_view), config, seconde=5)
+    if config['obi']['noprogressbar'] == False:
+        pb = ProgressBar(len(o_view), config)
+    else:
+        pb = None
 
     try:
 
@@ -354,14 +362,16 @@ def run(config):
         sequenceTagger = sequenceTaggerGenerator(config, taxo=taxo)
         for i in range(len(o_view)):
             PyErr_CheckSignals()
-            pb(i)
+            if pb is not None:
+                pb(i)
             sequenceTagger(o_view[i])
 
     except Exception, e:
         raise RollbackException("obi annotate error, rollbacking view: "+str(e), o_view)
 
-    pb(i, force=True)
-    print("", file=sys.stderr)
+    if pb is not None:
+        pb(i, force=True)
+        print("", file=sys.stderr)
     
     # Save command config in View and DMS comments
     command_line = " ".join(sys.argv[1:])
@@ -371,15 +381,21 @@ def run(config):
         input_dms_name.append(config['obi']['taxoURI'].split("/")[-3])
         input_view_name.append("taxonomy/"+config['obi']['taxoURI'].split("/")[-1])
     o_view.write_config(config, "annotate", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
-    output[0].record_command_line(command_line)
+    o_dms.record_command_line(command_line)
 
     #print("\n\nOutput view:\n````````````", file=sys.stderr)
     #print(repr(o_view), file=sys.stderr)
 
-    # If the input and the output DMS are different, delete the temporary imported view used to create the final view
-    if i_dms != o_dms:
+    # stdout output: write to buffer
+    if type(output_0)==BufferedWriter:
+        logger("info", "Printing to output...")
+        o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
+        o_view.close()
+
+    # If the input and the output DMS are different or if stdout output, delete the temporary imported view used to create the final view
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
         View.delete_view(o_dms, imported_view_name)
-        o_dms.close()
-    i_dms.close()
+        o_dms.close(force=True)
+    i_dms.close(force=True)
 
     logger("info", "Done.")

python/obitools3/commands/build_ref_db.pyx

@@ -4,14 +4,16 @@ from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
 from obitools3.dms.dms cimport DMS
 from obitools3.dms.view import RollbackException
 from obitools3.dms.capi.build_reference_db cimport build_reference_db
-from obitools3.apps.optiongroups import addMinimalInputOption, addTaxonomyOption, addMinimalOutputOption
+from obitools3.apps.optiongroups import addMinimalInputOption, addTaxonomyOption, addMinimalOutputOption, addNoProgressBarOption
 from obitools3.uri.decode import open_uri
 from obitools3.apps.config import logger
 from obitools3.utils cimport tobytes, str2bytes
 from obitools3.dms.view.view cimport View
 from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
 
+from io import BufferedWriter
 import sys
+from cpython.exc cimport PyErr_CheckSignals
 
 
 __title__="Tag a set of sequences for PCR and sequencing errors identification"
@@ -22,6 +24,7 @@ def addOptions(parser):
     addMinimalInputOption(parser)
     addTaxonomyOption(parser)
     addMinimalOutputOption(parser)
+    addNoProgressBarOption(parser)
  
     group = parser.add_argument_group('obi build_ref_db specific options')
 
@@ -56,17 +59,20 @@ def run(config):
     if output is None:
         raise Exception("Could not create output")
     o_dms = output[0]
+    output_0 = output[0]
     final_o_view_name = output[1]
     
-    # If the input and output DMS are not the same, build the database creating a temporary view that will be exported to 
+    # If stdout output or the input and output DMS are not the same, build the database creating a temporary view that will be exported to 
     # the right DMS and deleted in the other afterwards.
-    if i_dms != o_dms:
-        temporary_view_name = final_o_view_name
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
+        temporary_view_name = b"temp"
         i=0
         while temporary_view_name in i_dms:  # Making sure view name is unique in input DMS
-            temporary_view_name = final_o_view_name+b"_"+str2bytes(str(i))
+            temporary_view_name = temporary_view_name+b"_"+str2bytes(str(i))
             i+=1
         o_view_name = temporary_view_name
+        if type(output_0)==BufferedWriter:
+            o_dms = i_dms
     else:
         o_view_name = final_o_view_name
 
@@ -80,26 +86,33 @@ def run(config):
     input_dms_name.append(config['obi']['taxoURI'].split("/")[-3])
     input_view_name.append("taxonomy/"+config['obi']['taxoURI'].split("/")[-1])
     comments = View.print_config(config, "build_ref_db", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
-
+    
     if build_reference_db(i_dms.name_with_full_path, tobytes(i_view_name), tobytes(taxonomy_name), tobytes(o_view_name), comments, config['build_ref_db']['threshold']) < 0:
         raise Exception("Error building a reference database")
     
     # If the input and output DMS are not the same, export result view to output DMS
     if i_dms != o_dms:
         View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, final_o_view_name)
-    
+
+    # stdout output: write to buffer
+    if type(output_0)==BufferedWriter:
+        logger("info", "Printing to output...")
+        o_view = o_dms[o_view_name]
+        o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
+        o_view.close()
+
     # Save command config in DMS comments
     o_dms.record_command_line(command_line)
 
     #print("\n\nOutput view:\n````````````", file=sys.stderr)
     #print(repr(o_dms[final_o_view_name]), file=sys.stderr)
 
-    # If the input and the output DMS are different, delete the temporary result view in the input DMS
-    if i_dms != o_dms:
+    # If the input and the output DMS are different or if stdout output, delete the temporary imported view used to create the final view
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
         View.delete_view(i_dms, o_view_name)
-        o_dms.close()
+        o_dms.close(force=True)
     
-    i_dms.close()
+    i_dms.close(force=True)
 
     logger("info", "Done.")
     

python/obitools3/commands/cat.pyx

@@ -0,0 +1,164 @@
+#cython: language_level=3
+
+from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
+from obitools3.dms import DMS
+from obitools3.dms.view.view cimport View
+from obitools3.uri.decode import open_uri
+from obitools3.apps.optiongroups import addMinimalOutputOption, addNoProgressBarOption
+from obitools3.dms.view import RollbackException
+from obitools3.apps.config import logger
+from obitools3.utils cimport str2bytes
+from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
+from obitools3.dms.view.view cimport View
+from obitools3.dms.capi.obiview cimport NUC_SEQUENCE_COLUMN, REVERSE_SEQUENCE_COLUMN, \
+                                        QUALITY_COLUMN, REVERSE_QUALITY_COLUMN
+from obitools3.dms.capi.obitypes cimport OBI_SEQ, OBI_QUAL
+from obitools3.dms.column.column cimport Column
+
+from io import BufferedWriter
+import time
+import sys
+ 
+from cpython.exc cimport PyErr_CheckSignals
+
+
+__title__="Concatenate views."
+
+ 
+def addOptions(parser):
+    
+    addMinimalOutputOption(parser)
+    addNoProgressBarOption(parser)
+
+    group=parser.add_argument_group('obi cat specific options')
+
+    group.add_argument("-c",
+                       action="append", dest="cat:views_to_cat",
+                       metavar="<VIEW_NAME>",
+                       default=[],
+                       type=str,
+                       help="URI of a view to concatenate. (e.g. 'my_dms/my_view'). "
+                            "Several -c options can be used on the same "
+                            "command line.")
+
+     
+def run(config):
+     
+    DMS.obi_atexit()
+    
+    logger("info", "obi cat")
+
+    # Check the views to concatenate
+    idms_list = []
+    iview_list = []
+    total_len = 0
+    remove_qual = False
+    remove_rev_qual = False
+    v_type = View_NUC_SEQS
+    for v_uri in config["cat"]["views_to_cat"]:
+        input = open_uri(v_uri)
+        if input is None:
+            raise Exception("Could not read input view")
+        i_dms = input[0]
+        i_view = input[1]
+        if input[2] != View_NUC_SEQS:  # Check view type (output view is nuc_seqs view if all input view are nuc_seqs view)
+            v_type = View
+        if QUALITY_COLUMN not in i_view: # Check if keep quality column in output view (if all input views have it)
+            remove_qual = True
+        if REVERSE_QUALITY_COLUMN not in i_view: # same as above for reverse quality
+            remove_rev_qual = True
+        total_len += len(i_view)
+        idms_list.append(i_dms)
+        iview_list.append(i_view.name)
+        i_view.close()
+
+    # Open the output: only the DMS
+    output = open_uri(config['obi']['outputURI'],
+                      input=False, 
+                      newviewtype=v_type)
+    if output is None:
+        raise Exception("Could not create output view")
+    o_dms = output[0]
+    output_0 = output[0]
+    o_view = output[1]
+    
+    # stdout output
+    if type(output_0)==BufferedWriter: 
+        o_dms = i_dms
+    
+    # Initialize quality columns and their associated sequence columns if needed
+    if type(output_0) != BufferedWriter: 
+        if not remove_qual:
+            if NUC_SEQUENCE_COLUMN not in o_view:
+                Column.new_column(o_view, NUC_SEQUENCE_COLUMN, OBI_SEQ)
+            Column.new_column(o_view, QUALITY_COLUMN, OBI_QUAL, associated_column_name=NUC_SEQUENCE_COLUMN, associated_column_version=o_view[NUC_SEQUENCE_COLUMN].version)    
+        if not remove_rev_qual:
+            Column.new_column(o_view, REVERSE_SEQUENCE_COLUMN, OBI_SEQ)
+            Column.new_column(o_view, REVERSE_QUALITY_COLUMN, OBI_QUAL, associated_column_name=REVERSE_SEQUENCE_COLUMN, associated_column_version=o_view[REVERSE_SEQUENCE_COLUMN].version)
+        
+    # Initialize multiple elements columns
+    if type(output_0)==BufferedWriter: 
+        dict_cols = {}
+        for v_uri in config["cat"]["views_to_cat"]:
+            v = open_uri(v_uri)[1]
+            for coln in v.keys():
+                col = v[coln]
+                if v[coln].nb_elements_per_line > 1:
+                    if coln not in dict_cols:
+                        dict_cols[coln] = {}
+                        dict_cols[coln]['eltnames'] = set(v[coln].elements_names)
+                        dict_cols[coln]['nbelts'] = v[coln].nb_elements_per_line
+                        dict_cols[coln]['obitype'] = v[coln].data_type_int
+                    else:
+                        dict_cols[coln]['eltnames'] = set(v[coln].elements_names + list(dict_cols[coln]['eltnames']))
+                        dict_cols[coln]['nbelts'] = len(dict_cols[coln]['eltnames'])
+            v.close()            
+        for coln in dict_cols:
+            Column.new_column(o_view, coln, dict_cols[coln]['obitype'], 
+                              nb_elements_per_line=dict_cols[coln]['nbelts'], elements_names=list(dict_cols[coln]['eltnames']))
+    
+    # Initialize the progress bar
+    if not config['obi']['noprogressbar']:
+        pb = ProgressBar(total_len, config)
+    else:
+        pb = None
+    
+    i = 0
+    for v_uri in config["cat"]["views_to_cat"]:
+        v = open_uri(v_uri)[1]
+        for entry in v:
+            PyErr_CheckSignals()
+            if pb is not None:
+                pb(i)
+            if type(output_0)==BufferedWriter: 
+                rep = repr(entry)
+                output_0.write(str2bytes(rep)+b"\n")
+            else:
+                o_view[i] = entry
+            i+=1
+        v.close()
+
+    # Deletes quality columns if needed
+    if type(output_0)!=BufferedWriter: 
+        if QUALITY_COLUMN in o_view and remove_qual :
+            o_view.delete_column(QUALITY_COLUMN)
+        if REVERSE_QUALITY_COLUMN in o_view and remove_rev_qual :
+            o_view.delete_column(REVERSE_QUALITY_COLUMN)
+    
+    if pb is not None:
+        pb(i, force=True)
+        print("", file=sys.stderr)
+    
+    # Save command config in DMS comments
+    command_line = " ".join(sys.argv[1:])
+    o_view.write_config(config, "cat", command_line, input_dms_name=[d.name for d in idms_list], input_view_name=[vname for vname in iview_list])
+    o_dms.record_command_line(command_line)
+
+    #print("\n\nOutput view:\n````````````", file=sys.stderr)
+    #print(repr(view), file=sys.stderr)
+
+    for d in idms_list:
+        d.close(force=True)
+    o_dms.close(force=True)
+    
+    logger("info", "Done.")

python/obitools3/commands/clean.pyx

@@ -4,13 +4,14 @@ from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
 from obitools3.dms.dms cimport DMS
 from obitools3.dms.view import RollbackException
 from obitools3.dms.capi.obiclean cimport obi_clean
-from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption
+from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption, addNoProgressBarOption
 from obitools3.uri.decode import open_uri
 from obitools3.apps.config import logger
 from obitools3.utils cimport tobytes, str2bytes
 from obitools3.dms.view.view cimport View
 from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
 
+from io import BufferedWriter
 import sys
 
 
@@ -21,7 +22,8 @@ def addOptions(parser):
 
     addMinimalInputOption(parser)
     addMinimalOutputOption(parser)
- 
+    addNoProgressBarOption(parser)
+    
     group = parser.add_argument_group('obi clean specific options')
 
     group.add_argument('--distance', '-d',
@@ -36,8 +38,7 @@ def addOptions(parser):
                        dest="clean:sample-tag-name",
                        metavar="<SAMPLE TAG NAME>",
                        type=str,
-                       default="merged_sample",
-                       help="Name of the tag where sample counts are kept.")
+                       help="Name of the tag where merged sample count informations are kept (typically generated by obi uniq, usually MERGED_sample, default: None).")
     
     group.add_argument('--ratio', '-r',
                        action="store", dest="clean:ratio",
@@ -89,17 +90,20 @@ def run(config):
     if output is None:
         raise Exception("Could not create output")
     o_dms = output[0]
+    output_0 = output[0]
     final_o_view_name = output[1]
     
-    # If the input and output DMS are not the same, run obiclean creating a temporary view that will be exported to 
+    # If stdout output or the input and output DMS are not the same, create a temporary view that will be exported to 
     # the right DMS and deleted in the other afterwards.
-    if i_dms != o_dms:
-        temporary_view_name = final_o_view_name
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
+        temporary_view_name = b"temp"
         i=0
         while temporary_view_name in i_dms:  # Making sure view name is unique in input DMS
-            temporary_view_name = final_o_view_name+b"_"+str2bytes(str(i))
+            temporary_view_name = temporary_view_name+b"_"+str2bytes(str(i))
             i+=1
         o_view_name = temporary_view_name
+        if type(output_0)==BufferedWriter:
+            o_dms = i_dms
     else:
         o_view_name = final_o_view_name
         
@@ -107,6 +111,9 @@ def run(config):
     command_line = " ".join(sys.argv[1:])
     comments = View.print_config(config, "clean", command_line, input_dms_name=[i_dms_name], input_view_name=[i_view_name])
 
+    if 'sample-tag-name' not in config['clean']:
+        config['clean']['sample-tag-name'] = ""
+        
     if obi_clean(i_dms.name_with_full_path, tobytes(i_view_name), tobytes(config['clean']['sample-tag-name']), tobytes(o_view_name), comments, \
               config['clean']['distance'], config['clean']['ratio'], config['clean']['heads-only'], config['clean']['thread-count']) < 0:
         raise Exception("Error running obiclean")
@@ -114,18 +121,25 @@ def run(config):
     # If the input and output DMS are not the same, export result view to output DMS
     if i_dms != o_dms:
         View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, final_o_view_name)
-    
+
+    # stdout output: write to buffer
+    if type(output_0)==BufferedWriter:
+        logger("info", "Printing to output...")
+        o_view = o_dms[o_view_name]
+        o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
+        o_view.close()
+
     # Save command config in DMS comments
     o_dms.record_command_line(command_line)
 
     #print("\n\nOutput view:\n````````````", file=sys.stderr)
     #print(repr(o_dms[final_o_view_name]), file=sys.stderr)
 
-    # If the input and the output DMS are different, delete the temporary result view in the input DMS
-    if i_dms != o_dms:
+    # If the input and the output DMS are different or if stdout output, delete the temporary imported view used to create the final view
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
         View.delete_view(i_dms, o_view_name)
-        o_dms.close()
+        o_dms.close(force=True)
     
-    i_dms.close()
+    i_dms.close(force=True)
 
     logger("info", "Done.")

python/obitools3/commands/clean_dms.pyx

@@ -21,7 +21,10 @@ def run(config):
     
     logger("info", "obi clean_dms")
     
-    if obi_clean_dms(tobytes(config['obi']['inputURI'])) < 0 :
+    dms_path = tobytes(config['obi']['inputURI'])
+    if b'.obidms' in dms_path:
+        dms_path = dms_path.split(b'.obidms')[0]
+    if obi_clean_dms(dms_path) < 0 :
         raise Exception("Error cleaning DMS", config['obi']['inputURI'])
 
     logger("info", "Done.")

python/obitools3/commands/count.pyx

@@ -22,7 +22,7 @@ def addOptions(parser):
     group.add_argument('-s','--sequence',
                         action="store_true", dest="count:sequence",
                         default=False,
-                        help="Prints only the number of sequence records.")
+                        help="Prints only the number of sequence records (much faster, default: False).")
  
     group.add_argument('-a','--all',
                         action="store_true", dest="count:all",
@@ -56,3 +56,5 @@ def run(config):
         print(count2)
     else:
         print(count1)
+    
+    input[0].close(force=True)

python/obitools3/commands/ecopcr.pyx

@@ -5,10 +5,10 @@ from obitools3.dms.dms cimport DMS
 from obitools3.dms.capi.obidms cimport OBIDMS_p
 from obitools3.dms.view import RollbackException
 from obitools3.dms.capi.obiecopcr cimport obi_ecopcr
-from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption, addTaxonomyOption
+from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption, addTaxonomyOption, addNoProgressBarOption
 from obitools3.uri.decode import open_uri
 from obitools3.apps.config import logger
-from obitools3.utils cimport tobytes
+from obitools3.utils cimport tobytes, str2bytes
 from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
 from obitools3.dms.view import View
 
@@ -16,6 +16,7 @@ from libc.stdlib  cimport malloc, free
 from libc.stdint  cimport int32_t
 
 import sys
+from io import BufferedWriter
 
 
 __title__="in silico PCR"
@@ -27,6 +28,7 @@ def addOptions(parser):
     addMinimalInputOption(parser)
     addTaxonomyOption(parser)
     addMinimalOutputOption(parser)
+    addNoProgressBarOption(parser)
 
  
     group = parser.add_argument_group('obi ecopcr specific options')
@@ -35,13 +37,15 @@ def addOptions(parser):
                        action="store", dest="ecopcr:primer1",
                        metavar='<PRIMER>',
                        type=str,
-                       help="Forward primer.")
+                       required=True,
+                       help="Forward primer, length must be less than or equal to 32")
 
     group.add_argument('--primer2', '-R',
                        action="store", dest="ecopcr:primer2",
                        metavar='<PRIMER>',
                        type=str,
-                       help="Reverse primer.")
+                       required=True,
+                       help="Reverse primer, length must be less than or equal to 32")
 
     group.add_argument('--error', '-e',
                        action="store", dest="ecopcr:error",
@@ -107,14 +111,20 @@ def addOptions(parser):
                        help="Defines the method used for estimating the Tm (melting temperature) between the primers and their corresponding "
                             "target sequences. SANTALUCIA: 1, or OWCZARZY: 2. Default: 1.")
 
+    group.add_argument('--keep-primers', '-p',
+                       action="store_true", 
+                       dest="ecopcr:keep-primers",
+                       default=False,
+                       help="Whether to keep the primers attached to the output sequences (default: the primers are cut out).")
+
     group.add_argument('--keep-nucs', '-D',
                        action="store", 
                        dest="ecopcr:keep-nucs",
-                       metavar="<INTEGER>",
+                       metavar="<N>",
                        type=int,
                        default=0,
-                       help="Keeps the specified number of nucleotides on each side of the in silico amplified sequences, "
-                            "(already including the amplified DNA fragment plus the two target sequences of the primers).")
+                       help="Keeps N nucleotides on each side of the in silico amplified sequences, "
+                            "not including the primers (implying that primers are automatically kept if N > 0).")
 
     group.add_argument('--kingdom-mode', '-k',
                        action="store_true", 
@@ -161,11 +171,20 @@ def run(config):
     if output is None:
         raise Exception("Could not create output")
     o_dms = output[0]
+    output_0 = output[0]
     o_dms_name = output[0].name
     o_view_name = output[1]
 
     # Read taxonomy name    
     taxonomy_name = config['obi']['taxoURI'].split("/")[-1]   # Robust in theory
+
+    # If stdout output create a temporary view in the input dms that will be deleted afterwards.
+    if type(output_0)==BufferedWriter:
+        o_dms = i_dms
+        o_view_name = b"temp"
+        while o_view_name in i_dms:   # Making sure view name is unique in input DMS
+            o_view_name = o_view_name+b"_"+str2bytes(str(i))
+            i+=1
     
     # Save command config in View comments
     command_line = " ".join(sys.argv[1:])
@@ -185,7 +204,7 @@ def run(config):
                   config['ecopcr']['min-length'], config['ecopcr']['max-length'], \
                   restrict_to_taxids_p, ignore_taxids_p, \
                   config['ecopcr']['circular'], config['ecopcr']['salt-concentration'], config['ecopcr']['salt-correction-method'], \
-                  config['ecopcr']['keep-nucs'], config['ecopcr']['kingdom-mode']) < 0:
+                  config['ecopcr']['keep-nucs'], config['ecopcr']['keep-primers'], config['ecopcr']['kingdom-mode']) < 0:
         raise Exception("Error running ecopcr")
 
     # Save command config in DMS comments
@@ -193,10 +212,22 @@ def run(config):
 
     free(restrict_to_taxids_p)
     free(ignore_taxids_p)
-    
+
+    # stdout output: write to buffer
+    if type(output_0)==BufferedWriter:
+        logger("info", "Printing to output...")
+        o_view = o_dms[o_view_name]
+        o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
+        o_view.close()
+
     #print("\n\nOutput view:\n````````````", file=sys.stderr)
     #print(repr(o_dms[o_view_name]), file=sys.stderr)
 
-    o_dms.close()
+    # If stdout output, delete the temporary result view in the input DMS
+    if type(output_0)==BufferedWriter:
+        View.delete_view(i_dms, o_view_name)
+
+    i_dms.close(force=True)
+    o_dms.close(force=True)
 
     logger("info", "Done.")

python/obitools3/commands/ecotag.pyx

@@ -4,7 +4,7 @@ from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
 from obitools3.dms.dms cimport DMS
 from obitools3.dms.view import RollbackException
 from obitools3.dms.capi.obiecotag cimport obi_ecotag
-from obitools3.apps.optiongroups import addMinimalInputOption, addTaxonomyOption, addMinimalOutputOption
+from obitools3.apps.optiongroups import addMinimalInputOption, addTaxonomyOption, addMinimalOutputOption, addNoProgressBarOption
 from obitools3.uri.decode import open_uri
 from obitools3.apps.config import logger
 from obitools3.utils cimport tobytes, str2bytes
@@ -12,6 +12,7 @@ from obitools3.dms.view.view cimport View
 from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
 
 import sys
+from io import BufferedWriter
 
 
 __title__="Taxonomic assignment of sequences"
@@ -22,6 +23,7 @@ def addOptions(parser):
     addMinimalInputOption(parser)
     addTaxonomyOption(parser)
     addMinimalOutputOption(parser)
+    addNoProgressBarOption(parser)
  
     group = parser.add_argument_group('obi ecotag specific options')
 
@@ -39,6 +41,17 @@ def addOptions(parser):
                       help="Minimum identity to consider for assignment, as a normalized identity, e.g. 0.95 for an identity of 95%%. "
                            "Default: 0.00 (no threshold).")
 
+    group.add_argument('--minimum-circle','-c',
+                      action="store", dest="ecotag:bubble_threshold",
+                      metavar='<CIRCLE_THRESHOLD>',
+                      default=0.99,
+                      type=float,
+                      help="Minimum identity considered for the assignment circle "
+                           "(sequence is assigned to the LCA of all sequences within a similarity circle of the best matches; "
+                           "the threshold for this circle is the highest value between <CIRCLE_THRESHOLD> and the best assignment score found for the query sequence). "
+                           "Give value as a normalized identity, e.g. 0.95 for an identity of 95%%. "
+                           "Default: 0.99.")
+
 def run(config):
         
     DMS.obi_atexit()
@@ -64,10 +77,9 @@ def run(config):
     ref_view_name = ref[1]
 
     # Check that the threshold demanded is greater than or equal to the threshold used to build the reference database
-    if config['ecotag']['threshold'] < eval(i_dms[ref_view_name].comments["ref_db_threshold"]) :
-        print("Error: The threshold demanded (%f) is lower than the threshold used to build the reference database (%f).", 
-              config['ecotag']['threshold'], i_dms[ref_view_name].comments["ref_db_threshold"])
-
+    if config['ecotag']['bubble_threshold'] < eval(ref_dms[ref_view_name].comments["ref_db_threshold"]) :
+        raise Exception(f"Error: The threshold demanded ({config['ecotag']['bubble_threshold']}) is lower than the threshold used to build the reference database ({float(ref_dms[ref_view_name].comments['ref_db_threshold'])}).")
+    
     # Open the output: only the DMS
     output = open_uri(config['obi']['outputURI'],
                       input=False,
@@ -75,17 +87,19 @@ def run(config):
     if output is None:
         raise Exception("Could not create output")
     o_dms = output[0]
+    output_0 = output[0]
     final_o_view_name = output[1]
     
-    # If the input and output DMS are not the same, run ecotag creating a temporary view that will be exported to 
-    # the right DMS and deleted in the other afterwards.
-    if i_dms != o_dms:
-        temporary_view_name = final_o_view_name
+    # If stdout output or the input and output DMS are not the same, create a temporary view that will be exported and deleted.
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
+        temporary_view_name = b"temp"
         i=0
         while temporary_view_name in i_dms:  # Making sure view name is unique in input DMS
-            temporary_view_name = final_o_view_name+b"_"+str2bytes(str(i))
+            temporary_view_name = temporary_view_name+b"_"+str2bytes(str(i))
             i+=1
         o_view_name = temporary_view_name
+        if type(output_0)==BufferedWriter:
+            o_dms = i_dms
     else:
         o_view_name = final_o_view_name
 
@@ -107,10 +121,11 @@ def run(config):
     comments = View.print_config(config, "ecotag", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
 
     if obi_ecotag(i_dms.name_with_full_path, tobytes(i_view_name), \
-                  tobytes(ref_dms_name), tobytes(ref_view_name), \
-                  tobytes(taxo_dms_name), tobytes(taxonomy_name), \
-                  tobytes(o_view_name), comments, 
-                  config['ecotag']['threshold']) < 0:
+                  ref_dms.name_with_full_path, tobytes(ref_view_name), \
+                  taxo_dms.name_with_full_path, tobytes(taxonomy_name), \
+                  tobytes(o_view_name), comments, \
+                  config['ecotag']['threshold'], \
+                  config['ecotag']['bubble_threshold']) < 0:
         raise Exception("Error running ecotag")
     
     # If the input and output DMS are not the same, export result view to output DMS
@@ -120,15 +135,24 @@ def run(config):
     # Save command config in DMS comments
     o_dms.record_command_line(command_line)
 
+    # stdout output: write to buffer
+    if type(output_0)==BufferedWriter:
+        logger("info", "Printing to output...")
+        o_view = o_dms[o_view_name]
+        o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
+        o_view.close()
+
     #print("\n\nOutput view:\n````````````", file=sys.stderr)
     #print(repr(o_dms[final_o_view_name]), file=sys.stderr)
 
-    # If the input and the output DMS are different, delete the temporary result view in the input DMS
-    if i_dms != o_dms:
+    # If the input and the output DMS are different or if stdout output, delete the temporary imported view used to create the final view
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
         View.delete_view(i_dms, o_view_name)
-        o_dms.close()
+        o_dms.close(force=True)
     
-    i_dms.close()
+    taxo_dms.close(force=True)
+    ref_dms.close(force=True)
+    i_dms.close(force=True)
     
     logger("info", "Done.")
 

python/obitools3/commands/export.pyx

@@ -59,13 +59,23 @@ def run(config):
      # Check that the input view has the type NUC_SEQS if needed    # TODO discuss, maybe bool property
     if (output[2] == Nuc_Seq) and (iview.type != b"NUC_SEQS_VIEW") :  # Nuc_Seq_Stored? TODO
         raise Exception("Error: the view to export in fasta or fastq format is not a NUC_SEQS view")
-   
+    
+    if config['obi']['only'] is not None:
+        withoutskip = min(input[4], config['obi']['only'])
+    else:
+        withoutskip = input[4]
+     
+    if config['obi']['skip'] is not None:
+        skip = min(input[4], config['obi']['skip'])
+    else:
+        skip = 0
+    
     # Initialize the progress bar
     if config['obi']['noprogressbar']:
         pb = None
     else:
-        pb = ProgressBar(len(iview), config, seconde=5)
-    
+        pb = ProgressBar(withoutskip - skip, config)
+
     i=0
     for seq in iview :
         PyErr_CheckSignals()
@@ -79,14 +89,14 @@ def run(config):
 
     if pb is not None:
         pb(i, force=True)
-    print("", file=sys.stderr)
+        print("", file=sys.stderr)
 
     # TODO save command in input dms?
     
     if not BrokenPipeError and not IOError:
         output_object.close()
     iview.close()
-    input[0].close()
+    input[0].close(force=True)
 
     logger("info", "Done.")
 

python/obitools3/commands/grep.pyx

@@ -4,7 +4,7 @@ from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
 from obitools3.dms import DMS
 from obitools3.dms.view.view cimport View, Line_selection
 from obitools3.uri.decode import open_uri
-from obitools3.apps.optiongroups import addMinimalInputOption, addTaxonomyOption, addMinimalOutputOption
+from obitools3.apps.optiongroups import addMinimalInputOption, addTaxonomyOption, addMinimalOutputOption, addNoProgressBarOption
 from obitools3.dms.view import RollbackException
 from obitools3.apps.config import logger
 from obitools3.utils cimport tobytes, str2bytes
@@ -14,6 +14,7 @@ import time
 import re
 import sys
 import ast
+from io import BufferedWriter
 from cpython.exc cimport PyErr_CheckSignals
 
  
@@ -28,6 +29,7 @@ def addOptions(parser):
     addMinimalInputOption(parser)
     addTaxonomyOption(parser)
     addMinimalOutputOption(parser)
+    addNoProgressBarOption(parser)
 
     group=parser.add_argument_group("obi grep specific options")
  
@@ -36,14 +38,13 @@ def addOptions(parser):
                        metavar="<PREDICATE>",
                        default=[],
                        type=str,
-                       help="Warning: use bytes for character strings (b'text' instead of 'text'). "
-                            "Python boolean expression to be evaluated in the "
+                       help="Python boolean expression to be evaluated in the "
                             "sequence/line context. The attribute name can be "
                             "used in the expression as a variable name. "
                             "An extra variable named 'sequence' or 'line' refers "
                             "to the sequence or line object itself. "
                             "Several -p options can be used on the same "
-                            "commande line.")
+                            "command line.")
  
     group.add_argument("-S", "--sequence",
                        action="store", dest="grep:seq_pattern",
@@ -162,8 +163,7 @@ def obi_eval(compiled_expr, loc_env, line):
     return obi_eval_result
     
 
-def Filter_generator(options, tax_filter):
-    #taxfilter = taxonomyFilterGenerator(options)
+def Filter_generator(options, tax_filter, i_view):
 
     # Initialize conditions
     predicates = None
@@ -172,6 +172,9 @@ def Filter_generator(options, tax_filter):
     attributes = None
     if "attributes" in options and len(options["attributes"]) > 0:
         attributes = options["attributes"]
+        for attribute in attributes:
+            if attribute not in i_view:
+                return None
     lmax = None
     if "lmax" in options:
         lmax = options["lmax"]
@@ -197,6 +200,8 @@ def Filter_generator(options, tax_filter):
     if "attribute_patterns" in options and len(options["attribute_patterns"]) > 0:
         for p in options["attribute_patterns"]:
             attribute, pattern = p.split(":", 1)
+            if attribute not in i_view:
+                return None
             attribute_patterns[tobytes(attribute)] = re.compile(tobytes(pattern))
     
     def filter(line, loc_env):
@@ -301,16 +306,21 @@ def run(config):
     if output is None:
         raise Exception("Could not create output view")
     o_dms = output[0]
-    o_view_name_final = output[1]
-    o_view_name = o_view_name_final
-    
-    # If the input and output DMS are not the same, create output view in input DMS first, then export it
-    # to output DMS, making sure the temporary view name is unique in the input DMS 
-    if i_dms != o_dms:
+    output_0 = output[0]
+    final_o_view_name = output[1]
+
+    # If stdout output or the input and output DMS are not the same, create a temporary view that will be exported and deleted afterwards.
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
+        temporary_view_name = b"temp"
         i=0
-        while o_view_name in i_dms:
-            o_view_name = o_view_name_final+b"_"+str2bytes(str(i))
-            i+=1        
+        while temporary_view_name in i_dms:  # Making sure view name is unique in input DMS
+            temporary_view_name = temporary_view_name+b"_"+str2bytes(str(i))
+            i+=1
+        o_view_name = temporary_view_name
+        if type(output_0)==BufferedWriter:
+            o_dms = i_dms
+    else:
+        o_view_name = final_o_view_name
 
     if 'taxoURI' in config['obi'] and config['obi']['taxoURI'] is not None:
         taxo_uri = open_uri(config["obi"]["taxoURI"])
@@ -321,33 +331,49 @@ def run(config):
         taxo = None
 
     # Initialize the progress bar
-    pb = ProgressBar(len(i_view), config, seconde=5)
+    if config['obi']['noprogressbar'] == False:
+        pb = ProgressBar(len(i_view), config)
+    else:
+        pb = None
  
     # Apply filter
     tax_filter = Taxonomy_filter_generator(taxo, config["grep"])
-    filter = Filter_generator(config["grep"], tax_filter)
+    filter = Filter_generator(config["grep"], tax_filter, i_view)        
     selection = Line_selection(i_view)
-    for i in range(len(i_view)):
-        PyErr_CheckSignals()
-        pb(i)
-        line = i_view[i]
-                 
-        loc_env = {"sequence": line, "line": line, "taxonomy": taxo, "obi_eval_result": False}
-        
-        good = filter(line, loc_env)
- 
-        if good :
+    
+    if filter is None and config["grep"]["invert_selection"]: # all sequences are selected: filter is None if no line will be selected because some columns don't exist
+        for i in range(len(i_view)):
+            PyErr_CheckSignals()
+            if pb is not None:
+                pb(i)
             selection.append(i)
-
-    pb(i, force=True)
-    print("", file=sys.stderr)
+    
+    elif filter is not None :   # filter is None if no line will be selected because some columns don't exist
+        for i in range(len(i_view)):
+            PyErr_CheckSignals()
+            if pb is not None:
+                pb(i)
+            line = i_view[i]
+            
+            loc_env = {"sequence": line, "line": line, "taxonomy": taxo, "obi_eval_result": False}
+            
+            good = filter(line, loc_env)
+     
+            if good :
+                selection.append(i)
+   
+    if pb is not None:
+        pb(len(i_view), force=True)
+        print("", file=sys.stderr)
 
     # Create output view with the line selection
     try:
         o_view = selection.materialize(o_view_name)
     except Exception, e:
         raise RollbackException("obi grep error, rollbacking view: "+str(e), o_view)
-    
+
+    logger("info", "Grepped %d entries" % len(o_view))
+
     # Save command config in View and DMS comments
     command_line = " ".join(sys.argv[1:])
     input_dms_name=[input[0].name]
@@ -362,16 +388,22 @@ def run(config):
     # and delete the temporary view in the input DMS
     if i_dms != o_dms:
         o_view.close()
-        View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, o_view_name_final)
-        o_view = o_dms[o_view_name_final]
+        View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, final_o_view_name)
+        o_view = o_dms[final_o_view_name]
+    
+    # stdout output: write to buffer
+    if type(output_0)==BufferedWriter:
+        logger("info", "Printing to output...")
+        o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
+        o_view.close()
 
     #print("\n\nOutput view:\n````````````", file=sys.stderr)
     #print(repr(o_view), file=sys.stderr)
 
-    # If the input and the output DMS are different, delete the temporary imported view used to create the final view
-    if i_dms != o_dms:
+    # If the input and the output DMS are different or if stdout output, delete the temporary imported view used to create the final view
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
         View.delete_view(i_dms, o_view_name)
-        o_dms.close()
-    i_dms.close()
+        o_dms.close(force=True)
+    i_dms.close(force=True)
 
     logger("info", "Done.")

python/obitools3/commands/head.pyx

@@ -4,14 +4,15 @@ from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
 from obitools3.dms import DMS
 from obitools3.dms.view.view cimport View, Line_selection
 from obitools3.uri.decode import open_uri
-from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption
+from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption, addNoProgressBarOption
 from obitools3.dms.view import RollbackException
 from obitools3.apps.config import logger
 from obitools3.utils cimport str2bytes
 
 import time
 import sys
- 
+from io import BufferedWriter
+
 from cpython.exc cimport PyErr_CheckSignals
 
 
@@ -22,6 +23,7 @@ def addOptions(parser):
     
     addMinimalInputOption(parser)
     addMinimalOutputOption(parser)
+    addNoProgressBarOption(parser)
 
     group=parser.add_argument_group('obi head specific options')
 
@@ -53,31 +55,41 @@ def run(config):
     if output is None:
         raise Exception("Could not create output view")
     o_dms = output[0]
-    o_view_name_final = output[1]
-    o_view_name = o_view_name_final
+    output_0 = output[0]
+    final_o_view_name = output[1]
     
-    # If the input and output DMS are not the same, create output view in input DMS first, then export it
-    # to output DMS, making sure the temporary view name is unique in the input DMS 
-    if i_dms != o_dms:
+    # If stdout output or the input and output DMS are not the same, create a temporary view that will be exported and deleted.
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
+        temporary_view_name = b"temp"
         i=0
-        while o_view_name in i_dms:
-            o_view_name = o_view_name_final+b"_"+str2bytes(str(i))
-            i+=1        
+        while temporary_view_name in i_dms:  # Making sure view name is unique in input DMS
+            temporary_view_name = temporary_view_name+b"_"+str2bytes(str(i))
+            i+=1
+        o_view_name = temporary_view_name
+        if type(output_0)==BufferedWriter:
+            o_dms = i_dms
+    else:
+        o_view_name = final_o_view_name
     
     n = min(config['head']['count'], len(i_view))
 
     # Initialize the progress bar
-    pb = ProgressBar(n, config, seconde=5)
+    if config['obi']['noprogressbar'] == False:
+        pb = ProgressBar(n, config)
+    else:
+        pb = None
         
     selection = Line_selection(i_view)
     
     for i in range(n):
         PyErr_CheckSignals()
-        pb(i)
+        if pb is not None:
+            pb(i)
         selection.append(i)
 
-    pb(i, force=True)
-    print("", file=sys.stderr)
+    if pb is not None:
+        pb(i, force=True)
+        print("", file=sys.stderr)
 
     # Create output view with the line selection
     try:
@@ -94,16 +106,22 @@ def run(config):
     # and delete the temporary view in the input DMS
     if i_dms != o_dms:
         o_view.close()
-        View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, o_view_name_final)
-        o_view = o_dms[o_view_name_final]
+        View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, final_o_view_name)
+        o_view = o_dms[final_o_view_name]
+
+    # stdout output: write to buffer
+    if type(output_0)==BufferedWriter:
+        logger("info", "Printing to output...")
+        o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
+        o_view.close()
 
     #print("\n\nOutput view:\n````````````", file=sys.stderr)
     #print(repr(view), file=sys.stderr)
 
-    # If the input and the output DMS are different, delete the temporary imported view used to create the final view
-    if i_dms != o_dms:
+    # If the input and the output DMS are different or if stdout output, delete the temporary imported view used to create the final view
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
         View.delete_view(i_dms, o_view_name)
-        o_dms.close()
-    i_dms.close()
+        o_dms.close(force=True)
+    i_dms.close(force=True)
     
     logger("info", "Done.")

python/obitools3/commands/history.pyx

@@ -54,4 +54,5 @@ def run(config):
             print(bytes2str(entries.ascii_history))
         else:
             raise Exception("ASCII history only available for views")
-            
+    
+    input[0].close(force=True)

python/obitools3/commands/import.pyx

@@ -11,6 +11,7 @@ from obitools3.dms.column.column cimport Column
 from obitools3.dms.obiseq cimport Nuc_Seq
 from obitools3.dms import DMS
 from obitools3.dms.taxo.taxo cimport Taxonomy
+from obitools3.files.uncompress cimport CompressedFile
 
 
 from obitools3.utils cimport tobytes, \
@@ -24,13 +25,16 @@ from obitools3.dms.capi.obiview cimport VIEW_TYPE_NUC_SEQS, \
                                         DEFINITION_COLUMN, \
                                         QUALITY_COLUMN, \
                                         COUNT_COLUMN, \
-                                        TAXID_COLUMN
+                                        TAXID_COLUMN, \
+                                        MERGED_PREFIX, \
+                                        SCIENTIFIC_NAME_COLUMN
                                         
 from obitools3.dms.capi.obidms cimport obi_import_view
 
 from obitools3.dms.capi.obitypes cimport obitype_t, \
                                          OBI_VOID, \
-                                         OBI_QUAL
+                                         OBI_QUAL, \
+                                         OBI_STR
 
 from obitools3.dms.capi.obierrno cimport obi_errno
 
@@ -45,6 +49,8 @@ from obitools3.apps.config import logger
 
 from cpython.exc cimport PyErr_CheckSignals
 
+from io import BufferedWriter
+
 
 __title__="Imports sequences from different formats into a DMS"
  
@@ -65,6 +71,19 @@ def addOptions(parser):
     addTaxdumpInputOption(parser)
     addMinimalOutputOption(parser)
 
+    group = parser.add_argument_group('obi import specific options')
+
+    group.add_argument('--preread',
+                     action="store_true", dest="import:preread",
+                     default=False,
+                     help="Do a first readthrough of the dataset if it contains huge dictionaries (more than 100 keys) for "
+                          "a much faster import. This option is not recommended and will slow down the import in any other case.")
+
+    group.add_argument('--space-priority',
+                     action="store_true", dest="import:space_priority",
+                     default=False,
+                     help="If importing a view into another DMS, do it by importing each line, saving disk space if the original view "
+                          "has a line selection associated.")
 
 def run(config):
     
@@ -77,6 +96,7 @@ def run(config):
     cdef   obitype_t   new_type
     cdef   bint        get_quality
     cdef   bint        NUC_SEQS_view
+    cdef   bint        silva
     cdef   int         nb_elts
     cdef   object      d
     cdef   View        view
@@ -87,6 +107,8 @@ def run(config):
     cdef   Column      seq_col
     cdef   Column      qual_col
     cdef   Column      old_column
+    cdef   Column      sci_name_col
+    cdef   bytes       sci_name
     cdef   bint        rewrite
     cdef   dict        dcols
     cdef   int         skipping
@@ -120,7 +142,7 @@ def run(config):
         if entry_count > 0:
             logger("info", "Importing %d entries", entry_count)
         else:
-            logger("info", "Importing an unknow number of entries")
+            logger("info", "Importing an unknown number of entries")
         
         # TODO a bit dirty?
         if input[2]==Nuc_Seq or input[2]==View_NUC_SEQS:
@@ -130,7 +152,7 @@ def run(config):
     else:
         v = None
     
-    if config['obi']['taxdump'] or isinstance(input[1], View): 
+    if config['obi']['taxdump'] or (isinstance(input[1], View) and not config['import']['space_priority']): 
         dms_only=True
     else:
         dms_only=False
@@ -154,23 +176,24 @@ def run(config):
         taxo.write(taxo_name)
         taxo.close()
         o_dms.record_command_line(" ".join(sys.argv[1:]))
-        o_dms.close()
+        o_dms.close(force=True)
         logger("info", "Done.")
         return
 
-    # If importing a view between two DMS, use C API
-    if isinstance(input[1], View):
+    # If importing a view between two DMS and not wanting to save space if line selection in original view, use C API
+    if isinstance(input[1], View) and not config['import']['space_priority']:
         if obi_import_view(input[0].name_with_full_path, o_dms.name_with_full_path, input[1].name, tobytes((config['obi']['outputURI'].split('/'))[-1])) < 0 :
+            input[0].close(force=True)
+            output[0].close(force=True)
             raise Exception("Error importing a view in a DMS")
         o_dms.record_command_line(" ".join(sys.argv[1:]))
-        o_dms.close()
+        input[0].close(force=True)
+        output[0].close(force=True)
         logger("info", "Done.")
         return
 
     if entry_count >= 0:
-        pb = ProgressBar(entry_count, config, seconde=5)
-    
-    entries = input[1]
+        pb = ProgressBar(entry_count, config)
         
     NUC_SEQS_view = False
     if isinstance(output[1], View) :
@@ -185,9 +208,73 @@ def run(config):
         id_col = view[ID_COLUMN]
         def_col = view[DEFINITION_COLUMN]
         seq_col = view[NUC_SEQUENCE_COLUMN]
-        
+
+    # Prepare taxon scientific name if SILVA file
+    if 'inputformat' in config['obi'] and config['obi']['inputformat'] == b"silva":
+        silva = True
+        sci_name_col = Column.new_column(view, SCIENTIFIC_NAME_COLUMN, OBI_STR)
+    else:
+        silva = False
+    
     dcols = {}
+
+    # First read through the entries to prepare columns with dictionaries as they are very time-expensive to rewrite
+    if config['import']['preread']:
+        logger("info", "First readthrough...")
+        entries = input[1]
+        i = 0
+        dict_dict = {}
+        for entry in entries:
+            PyErr_CheckSignals()
         
+            if entry is None:  # error or exception handled at lower level, not raised because Python generators can't resume after any exception is raised
+                if config['obi']['skiperror']:
+                    i-=1
+                    continue
+                else:
+                    raise Exception("obi import error in first readthrough")
+            
+            if pb is not None:
+                pb(i)
+            elif not i%50000:
+                logger("info", "Read %d entries", i)
+    
+            for tag in entry :
+                newtag = tag
+                if tag[:7] == b"merged_":
+                    newtag = MERGED_PREFIX+tag[7:]
+                if type(entry[tag]) == dict :
+                    if tag in dict_dict:
+                        dict_dict[newtag][0].update(entry[tag].keys())
+                    else:
+                        dict_dict[newtag] = [set(entry[tag].keys()), get_obitype(entry[tag])]
+            i+=1
+        
+        if pb is not None:
+            pb(i, force=True)
+            print("", file=sys.stderr)
+       
+        for tag in dict_dict:
+            dcols[tag] = (Column.new_column(view, tag, dict_dict[tag][1], \
+                              nb_elements_per_line=len(dict_dict[tag][0]), \
+                              elements_names=list(dict_dict[tag][0])), \
+                          dict_dict[tag][1])
+    
+        
+        # Reinitialize the input
+        if isinstance(input[0], CompressedFile):
+            input_is_file = True
+        if entry_count >= 0:
+            pb = ProgressBar(entry_count, config)
+        try:
+            input[0].close()
+        except AttributeError:
+            pass
+        input = open_uri(config['obi']['inputURI'], force_file=input_is_file)
+        if input is None:
+            raise Exception("Could not open input URI")
+    
+    entries = input[1]
     i = 0
     for entry in entries :
         
@@ -195,7 +282,6 @@ def run(config):
 
         if entry is None:  # error or exception handled at lower level, not raised because Python generators can't resume after any exception is raised
             if config['obi']['skiperror']:
-                i-=1
                 continue
             else:
                 raise RollbackException("obi import error, rollbacking view", view)
@@ -204,115 +290,139 @@ def run(config):
             pb(i)
         elif not i%50000:
             logger("info", "Imported %d entries", i)
-              
-        if NUC_SEQS_view: 
-            id_col[i] = entry.id
-            def_col[i] = entry.definition
-            seq_col[i] = entry.seq
-            # Check if there is a sequencing quality associated by checking the first entry    # TODO haven't found a more robust solution yet
-            if i == 0:
-                get_quality = QUALITY_COLUMN in entry
+        
+        try:
+             
+            if NUC_SEQS_view: 
+                id_col[i] = entry.id           
+                def_col[i] = entry.definition
+                seq_col[i] = entry.seq
+                # Check if there is a sequencing quality associated by checking the first entry    # TODO haven't found a more robust solution yet
+                if i == 0:
+                    get_quality = QUALITY_COLUMN in entry
+                    if get_quality:
+                        Column.new_column(view, QUALITY_COLUMN, OBI_QUAL)
+                        qual_col = view[QUALITY_COLUMN]
                 if get_quality:
-                    Column.new_column(view, QUALITY_COLUMN, OBI_QUAL)
-                    qual_col = view[QUALITY_COLUMN]
-            if get_quality:
-                qual_col[i] = entry.quality
-         
-        for tag in entry :
-            
-            if tag != ID_COLUMN and tag != DEFINITION_COLUMN and tag != NUC_SEQUENCE_COLUMN and tag != QUALITY_COLUMN :  # TODO dirty 
-                                
-                value = entry[tag]
-                if tag == b"taxid":
-                    tag = TAXID_COLUMN
-                if tag == b"count":
-                    tag = COUNT_COLUMN
+                    qual_col[i] = entry.quality
                     
-                if tag not in dcols :
-                     
-                    value_type = type(value)
-                    nb_elts = 1
-                    value_obitype = OBI_VOID
-                     
-                    if value_type == dict or value_type == list :
-                        nb_elts = len(value)
-                        elt_names = list(value)
-                    else :
-                        nb_elts = 1
-                        elt_names = None
-                     
-                    value_obitype = get_obitype(value)
-                     
-                    if value_obitype != OBI_VOID :
-                        dcols[tag] = (Column.new_column(view, tag, value_obitype, nb_elements_per_line=nb_elts, elements_names=elt_names), value_obitype)
-                                                 
-                        # Fill value
-                        dcols[tag][0][i] = value
-                     
-                    # TODO else log error?
- 
-                else :
-         
-                    rewrite = False
- 
-                    # Check type adequation
-                    old_type = dcols[tag][1]
-                    new_type = OBI_VOID
-                    new_type = update_obitype(old_type, value)
-                    if old_type != new_type :
-                        rewrite = True
- 
-                    try:
-                        # Fill value
-                        dcols[tag][0][i] = value
-                     
-                    except IndexError :
-                                                 
+                # Parse taxon scientific name if SILVA file
+                if silva:
+                    sci_name = entry.definition.split(b";")[-1]
+                    sci_name_col[i] = sci_name
+             
+            for tag in entry :
+                
+                if tag != ID_COLUMN and tag != DEFINITION_COLUMN and tag != NUC_SEQUENCE_COLUMN and tag != QUALITY_COLUMN :  # TODO dirty 
+                                    
+                    value = entry[tag]
+                    if tag == b"taxid":
+                        tag = TAXID_COLUMN
+                    if tag == b"count":
+                        tag = COUNT_COLUMN
+                    if tag[:7] == b"merged_":
+                        tag = MERGED_PREFIX+tag[7:]
+                        
+                    if tag not in dcols :
+                         
                         value_type = type(value)
-                        old_column = dcols[tag][0]
-                        old_nb_elements_per_line = old_column.nb_elements_per_line
-                        new_nb_elements_per_line = 0
-                        old_elements_names = old_column.elements_names
-                        new_elements_names = None
+                        nb_elts = 1
+                        value_obitype = OBI_VOID
+                         
+                        if value_type == dict or value_type == list :
+                            nb_elts = len(value)
+                            elt_names = list(value)
+                        else :
+                            nb_elts = 1
+                            elt_names = None
+                         
+                        value_obitype = get_obitype(value)
+                         
+                        if value_obitype != OBI_VOID :
+                            dcols[tag] = (Column.new_column(view, tag, value_obitype, nb_elements_per_line=nb_elts, elements_names=elt_names), value_obitype)
+                                                     
+                            # Fill value
+                            if value_type == dict and nb_elts == 1:  # special case that makes the OBI3 create a 1 elt/line column which won't read a dict value
+                                value = value[list(value.keys())[0]]       # The solution is to transform the value in a simple atomic one acceptable by the column
+                            dcols[tag][0][i] = value
+                         
+                        # TODO else log error?
      
-                        #####################################################################
-                         
-                        # Check the length and keys of column lines if needed
-                        if value_type == dict :    # Check dictionary keys
-                            for k in value :
-                                if k not in old_elements_names :
-                                    new_elements_names = list(set(old_elements_names+[tobytes(k) for k in value]))
-                                    rewrite = True
-                                    break
-                         
-                        elif value_type == list or value_type == tuple :  # Check vector length
-                            if old_nb_elements_per_line < len(value) :
-                                new_nb_elements_per_line = len(value)
-                                rewrite = True
-                         
-                        #####################################################################
-                         
-                        if rewrite :
-                            if new_nb_elements_per_line == 0 and new_elements_names is not None :
-                                new_nb_elements_per_line = len(new_elements_names)
-                             
-                            # Reset obierrno 
-                            obi_errno = 0
- 
-                            dcols[tag] = (view.rewrite_column_with_diff_attributes(old_column.name, 
-                                                                                   new_data_type=new_type, 
-                                                                                   new_nb_elements_per_line=new_nb_elements_per_line,
-                                                                                   new_elements_names=new_elements_names,
-                                                                                   rewrite_last_line=False), 
-                                          new_type)
-                             
-                            # Update the dictionary:
-                            for t in dcols :
-                                dcols[t] = (view[t], dcols[t][1])
-                             
+                    else :
+             
+                        rewrite = False
+     
+                        # Check type adequation
+                        old_type = dcols[tag][1]
+                        new_type = OBI_VOID
+                        new_type = update_obitype(old_type, value)
+                        if old_type != new_type :
+                            rewrite = True
+     
+                        try:
+                            # Check that it's not the case where the first entry contained a dict of length 1 and now there is a new key                        
+                            if type(value) == dict and \
+                                dcols[tag][0].nb_elements_per_line == 1 \
+                                and set(dcols[tag][0].elements_names) != set(value.keys()) :
+                                raise IndexError  # trigger column rewrite
+                            
                             # Fill value
                             dcols[tag][0][i] = value
-                                    
+                         
+                        except IndexError :
+                                                     
+                            value_type = type(value)
+                            old_column = dcols[tag][0]
+                            old_nb_elements_per_line = old_column.nb_elements_per_line
+                            new_nb_elements_per_line = 0
+                            old_elements_names = old_column.elements_names
+                            new_elements_names = None
+         
+                            #####################################################################
+                             
+                            # Check the length and keys of column lines if needed
+                            if value_type == dict :    # Check dictionary keys
+                                for k in value :
+                                    if k not in old_elements_names :
+                                        new_elements_names = list(set(old_elements_names+[tobytes(k) for k in value]))
+                                        rewrite = True
+                                        break
+                             
+                            elif value_type == list or value_type == tuple :  # Check vector length
+                                if old_nb_elements_per_line < len(value) :
+                                    new_nb_elements_per_line = len(value)
+                                    rewrite = True
+                             
+                            #####################################################################
+                             
+                            if rewrite :
+                                if new_nb_elements_per_line == 0 and new_elements_names is not None :
+                                    new_nb_elements_per_line = len(new_elements_names)
+                                 
+                                # Reset obierrno 
+                                obi_errno = 0
+     
+                                dcols[tag] = (view.rewrite_column_with_diff_attributes(old_column.name, 
+                                                                                       new_data_type=new_type, 
+                                                                                       new_nb_elements_per_line=new_nb_elements_per_line,
+                                                                                       new_elements_names=new_elements_names,
+                                                                                       rewrite_last_line=False), 
+                                              new_type)
+                                 
+                                # Update the dictionary:
+                                for t in dcols :
+                                    dcols[t] = (view[t], dcols[t][1])
+                                 
+                                # Fill value
+                                dcols[tag][0][i] = value
+        
+        except Exception as e:
+            print("\nCould not import sequence id:", entry.id, "(error raised:", e, ")")
+            if 'skiperror' in config['obi'] and not config['obi']['skiperror']:
+                raise e
+            else:
+                pass
+        
         i+=1
  
     if pb is not None:
@@ -333,7 +443,7 @@ def run(config):
     except AttributeError:
         pass
     try:
-        output[0].close()
+        output[0].close(force=True)
     except AttributeError:
         pass
 

python/obitools3/commands/less.pyx

@@ -46,5 +46,5 @@ def run(config):
     process.wait()
 
     iview.close()
-    input[0].close()
+    input[0].close(force=True)
 

python/obitools3/commands/ls.pyx

@@ -31,24 +31,11 @@ def run(config):
     input = open_uri(config['obi']['inputURI'])
     if input is None:
         raise Exception("Could not read input")
-    if input[2] == DMS and not config['ls']['longformat']:
-        dms = input[0]
-        l = []
-        for view in input[0]:
-            l.append(tostr(view) + "\t(Date created: " + str(bytes2str_object(dms[view].comments["Date created"]))+")")
-        l.sort()
-        for v in l:
-            print(v)
+    
+    # Print representation
+    if config['ls']['longformat']:
+        print(input[1].repr_longformat())
     else:
         print(repr(input[1]))
-    if input[2] == DMS:
-        taxolist = ["\n### Taxonomies:"]
-        for t in Taxonomy.list_taxos(input[0]):
-            taxolist.append("\t"+tostr(t))
-        if len(taxolist) > 1:
-            for t in taxolist:
-                print(t)
-    if config['ls']['longformat'] and len(input[1].comments) > 0:
-        print("\n### Comments:")
-        print(str(input[1].comments))
-     
+    
+    input[0].close(force=True)

python/obitools3/commands/ngsfilter.pyx

@@ -2,10 +2,10 @@
 
 from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
 from obitools3.dms import DMS
-from obitools3.dms.view import RollbackException
+from obitools3.dms.view import RollbackException, View
 from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
 from obitools3.dms.column.column cimport Column, Column_line
-from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption
+from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption, addNoProgressBarOption
 from obitools3.uri.decode import open_uri
 from obitools3.apps.config import logger
 from obitools3.libalign._freeendgapfm import FreeEndGapFullMatch
@@ -13,17 +13,19 @@ from obitools3.libalign.apat_pattern import Primer_search
 from obitools3.dms.obiseq cimport Nuc_Seq
 from obitools3.dms.capi.obitypes cimport OBI_SEQ, OBI_QUAL
 from obitools3.dms.capi.apat cimport MAX_PATTERN
-from obitools3.utils cimport tobytes
+from obitools3.dms.capi.obiview cimport REVERSE_SEQUENCE_COLUMN, REVERSE_QUALITY_COLUMN
+from obitools3.utils cimport tobytes, str2bytes
 
 from libc.stdint cimport INT32_MAX
 from functools import reduce
 import math
 import sys
 from cpython.exc cimport PyErr_CheckSignals
+from io import BufferedWriter
 
 
-REVERSE_SEQ_COLUMN_NAME = b"REVERSE_SEQUENCE"      # used by alignpairedend tool
-REVERSE_QUALITY_COLUMN_NAME = b"REVERSE_QUALITY"   # used by alignpairedend tool
+#REVERSE_SEQ_COLUMN_NAME = b"REVERSE_SEQUENCE"      # used by alignpairedend tool
+#REVERSE_QUALITY_COLUMN_NAME = b"REVERSE_QUALITY"   # used by alignpairedend tool
 
 
 __title__="Assigns sequence records to the corresponding experiment/sample based on DNA tags and primers"
@@ -33,7 +35,8 @@ def addOptions(parser):
 
     addMinimalInputOption(parser)
     addMinimalOutputOption(parser)
- 
+    addNoProgressBarOption(parser)
+    
     group = parser.add_argument_group('obi ngsfilter specific options')
 
     group.add_argument('-t','--info-view',
@@ -41,7 +44,9 @@ def addOptions(parser):
                      metavar="<URI>",
                      type=str,
                      default=None,
-                     help="URI to the view containing the samples definition (with tags, primers, sample names,...)")
+                     required=True,
+                     help="URI to the view containing the samples definition (with tags, primers, sample names,...).\n"
+                          "\nWarning: primer lengths must be less than or equal to 32")
 
     group.add_argument('-R', '--reverse-reads',
                      action="store", dest="ngsfilter:reverse",
@@ -55,7 +60,12 @@ def addOptions(parser):
                      metavar="<URI>",
                      type=str,
                      default=None,
-                     help="URI to the view used to store the sequences unassigned to any sample")
+                     help="URI to the view used to store the sequences unassigned to any sample. Those sequences are untrimmed.")
+
+    group.add_argument('--no-tags',
+                     action="store_true", dest="ngsfilter:notags",
+                     default=False,
+                     help="Use this option if your experiment does not use tags to identify samples")
     
     group.add_argument('-e','--error',
                      action="store", dest="ngsfilter:error",
@@ -166,8 +176,15 @@ cdef read_info_view(info_view, max_errors=2, verbose=False, not_aligned=False):
     primer_list = []
     i=0
     for p in info_view:
+        
+        # Check primer length: should not be longer than 32, the max allowed by the apat lib
+        if len(p[b'forward_primer']) > 32:
+            raise RollbackException("Error: primers can not be longer than 32bp, rollbacking views")
+        if len(p[b'reverse_primer']) > 32:
+            raise RollbackException("Error: primers can not be longer than 32bp, rollbacking views")
+        
         forward=Primer(p[b'forward_primer'],
-                       len(p[b'forward_tag']) if p[b'forward_tag']!=b'-' else None,
+                       len(p[b'forward_tag']) if (b'forward_tag' in p and p[b'forward_tag']!=None) else None,
                        True,
                        max_errors=max_errors,
                        verbose=verbose,
@@ -178,7 +195,7 @@ cdef read_info_view(info_view, max_errors=2, verbose=False, not_aligned=False):
         infos[forward]=fp
         
         reverse=Primer(p[b'reverse_primer'],
-                       len(p[b'reverse_tag']) if p[b'reverse_tag']!=b'-' else None,
+                       len(p[b'reverse_tag']) if (b'reverse_tag' in p and p[b'reverse_tag']!=None) else None,
                        False,
                        max_errors=max_errors,
                        verbose=verbose,
@@ -213,10 +230,11 @@ cdef read_info_view(info_view, max_errors=2, verbose=False, not_aligned=False):
             rpp=rp.get(cf,{})
             rp[cf]=rpp
 
-        tags = (p[b'forward_tag'] if p[b'forward_tag']!=b'-' else None,
-                p[b'reverse_tag'] if p[b'reverse_tag']!=b'-' else None)
+        tags = (p[b'forward_tag'] if (b'forward_tag' in p and p[b'forward_tag']!=None) else None,
+                p[b'reverse_tag'] if (b'reverse_tag' in p and p[b'reverse_tag']!=None) else None)
         
-        assert tags not in dpp, \
+        if tags != (None, None):
+            assert tags not in dpp, \
                "Tag pair %s is already used with primer pairs: (%s,%s)" % (str(tags),forward,reverse)
         
         # Save additional data
@@ -234,7 +252,7 @@ cdef read_info_view(info_view, max_errors=2, verbose=False, not_aligned=False):
     return infos, primer_list
     
 
-cdef tuple annotate(sequences, infos, verbose=False):
+cdef tuple annotate(sequences, infos, no_tags, verbose=False):
         
     def sortMatch(match):
         if match[1] is None:
@@ -249,17 +267,12 @@ cdef tuple annotate(sequences, infos, verbose=False):
             return match[1][1]
     
     not_aligned = len(sequences) > 1
-    sequenceF = sequences[0]
-    sequenceR = None
-    if not not_aligned: 
-        final_sequence = sequenceF
-    else:
-        final_sequence = sequenceF.clone()   # TODO maybe not cloning and then deleting quality tags is more efficient
+    sequences[0] = sequences[0].clone()
 
     if not_aligned:
-        sequenceR = sequences[1]
-        final_sequence[REVERSE_SEQ_COLUMN_NAME] = sequenceR.seq             # used by alignpairedend tool
-        final_sequence[REVERSE_QUALITY_COLUMN_NAME] = sequenceR.quality     # used by alignpairedend tool
+        sequences[1] = sequences[1].clone()
+        sequences[0][REVERSE_SEQUENCE_COLUMN] = sequences[1].seq             # used by alignpairedend tool
+        sequences[0][REVERSE_QUALITY_COLUMN] = sequences[1].quality     # used by alignpairedend tool
 
     for seq in sequences:
         if hasattr(seq, "quality_array"): 
@@ -275,8 +288,6 @@ cdef tuple annotate(sequences, infos, verbose=False):
     
     # Try direct matching:
     directmatch = []
-    first_matched_seq = None
-    second_matched_seq = None
     for seq in sequences:
         new_seq = True
         pattern = 0
@@ -295,60 +306,96 @@ cdef tuple annotate(sequences, infos, verbose=False):
     directmatch = directmatch[0] if directmatch[0][1] is not None else None
 
     if directmatch is None:
-        final_sequence[b'error']=b'No primer match'
-        return False, final_sequence
+        if not_aligned:
+            sequences[0][REVERSE_SEQUENCE_COLUMN] = sequences[1].seq             # used by alignpairedend tool
+            sequences[0][REVERSE_QUALITY_COLUMN] = sequences[1].quality     # used by alignpairedend tool
+        sequences[0][b'error']=b'No primer match'
+        return False, sequences[0]
 
-    first_matched_seq = directmatch[2]
-    if id(first_matched_seq) == id(sequenceF) and not_aligned:
-        second_matched_seq = sequenceR
+    if id(directmatch[2]) == id(sequences[0]):
+        first_match_first_seq = True
     else:
-        second_matched_seq = sequenceF
-   
-    match = first_matched_seq[directmatch[1][1]:directmatch[1][2]]
+        first_match_first_seq = False
+       
+    match = directmatch[2][directmatch[1][1]:directmatch[1][2]]
     
     if not not_aligned:
-        final_sequence[b'seq_length_ori']=len(final_sequence)
+        sequences[0][b'seq_length_ori']=len(sequences[0])
     
-    if not not_aligned or id(first_matched_seq) == id(sequenceF):
-        final_sequence = final_sequence[directmatch[1][2]:]
+    if not not_aligned or first_match_first_seq:
+        sequences[0] = sequences[0][directmatch[1][2]:]
     else:
-        cut_seq = sequenceR[directmatch[1][2]:]
-        final_sequence[REVERSE_SEQ_COLUMN_NAME] = cut_seq.seq           # used by alignpairedend tool
-        final_sequence[REVERSE_QUALITY_COLUMN_NAME] = cut_seq.quality   # used by alignpairedend tool
+        sequences[1] = sequences[1][directmatch[1][2]:]
+        sequences[0][REVERSE_SEQUENCE_COLUMN] = sequences[1].seq           # used by alignpairedend tool
+        sequences[0][REVERSE_QUALITY_COLUMN] = sequences[1].quality   # used by alignpairedend tool
     
     if directmatch[0].forward:
-        final_sequence[b'direction']=b'forward'
-        final_sequence[b'forward_errors']=directmatch[1][0]
-        final_sequence[b'forward_primer']=directmatch[0].raw
-        final_sequence[b'forward_match']=match.seq
+        sequences[0][b'direction']=b'forward'
+        sequences[0][b'forward_errors']=directmatch[1][0]
+        sequences[0][b'forward_primer']=directmatch[0].raw
+        sequences[0][b'forward_match']=match.seq
         
     else:
-        final_sequence[b'direction']=b'reverse'
-        final_sequence[b'reverse_errors']=directmatch[1][0]
-        final_sequence[b'reverse_primer']=directmatch[0].raw
-        final_sequence[b'reverse_match']=match.seq
+        sequences[0][b'direction']=b'reverse'
+        sequences[0][b'reverse_errors']=directmatch[1][0]
+        sequences[0][b'reverse_primer']=directmatch[0].raw
+        sequences[0][b'reverse_match']=match.seq
 
     # Keep only paired reverse primer
-    infos = infos[directmatch[0]]    
-    
+    infos = infos[directmatch[0]]
+    reverse_primer = list(infos.keys())[0]
+    direct_primer = directmatch[0]
+        
     # If not aligned, look for other match in already computed matches (choose the one that makes the biggest amplicon)
     if not_aligned:
         i=1
         # TODO comment
-        while i<len(all_direct_matches) and (all_direct_matches[i][1] is None or all_direct_matches[i][0].forward == directmatch[0].forward or all_direct_matches[i][0] == directmatch[0]):
+        while i<len(all_direct_matches) and \
+            (all_direct_matches[i][1] is None or \
+             all_direct_matches[i][0].forward == directmatch[0].forward or \
+             all_direct_matches[i][0] == directmatch[0] or \
+             reverse_primer != all_direct_matches[i][0]) :
             i+=1
         if i < len(all_direct_matches):
             reversematch = all_direct_matches[i]
         else:
             reversematch = None
+        
+    # Cut reverse primer out of 1st matched seq if it contains it, because if it's also in the other sequence, the next step will "choose" only the one on the other sequence
+    if not_aligned:
+        # do it on same seq
+        if first_match_first_seq:
+            r = reverse_primer.revcomp(sequences[0])
+        else:
+            r = reverse_primer.revcomp(sequences[1]) 
+        if r is not None: # found
+            if first_match_first_seq :
+                sequences[0] = sequences[0][:r[1]]
+            else:
+                sequences[1] = sequences[1][:r[1]]
+                sequences[0][REVERSE_SEQUENCE_COLUMN] = sequences[1].seq           # used by alignpairedend tool
+                sequences[0][REVERSE_QUALITY_COLUMN] = sequences[1].quality   # used by alignpairedend tool
+        # do the same on the other seq
+        if first_match_first_seq: 
+            r = direct_primer.revcomp(sequences[1])
+        else:
+            r = direct_primer.revcomp(sequences[0])
+        if r is not None: # found
+            if first_match_first_seq:
+                sequences[1] = sequences[1][:r[1]]
+            else:
+                sequences[0] = sequences[0][:r[1]] 
+                sequences[0][REVERSE_SEQUENCE_COLUMN] = sequences[1].seq
+                sequences[0][REVERSE_QUALITY_COLUMN] = sequences[1].quality
+    
     
     # Look for other primer in the other direction on the sequence, or
     # If sequences are not already aligned and reverse primer not found in most likely sequence (the one without the forward primer), try matching on the same sequence than the first match (primer in the other direction)
     if not not_aligned or (not_aligned and (reversematch is None or reversematch[1] is None)):
-        if not not_aligned:
-            sequence_to_match = second_matched_seq
+        if not_aligned and first_match_first_seq:
+            seq_to_match = sequences[1]
         else:
-            sequence_to_match = first_matched_seq
+            seq_to_match = sequences[0]
         reversematch = []
         # Compute begin
         begin=directmatch[1][2]+1  # end of match + 1 on the same sequence
@@ -365,7 +412,7 @@ cdef tuple annotate(sequences, infos, verbose=False):
                 primer=p
             # Saving original primer as 4th member of the tuple to serve as correct key in infos dict even if it might have been reversed complemented
             # (3rd member already used by directmatch)
-            reversematch.append((primer, primer(sequence_to_match, same_sequence=not new_seq, pattern=pattern, begin=begin), None, p))
+            reversematch.append((primer, primer(seq_to_match, same_sequence=not new_seq, pattern=pattern, begin=begin), None, p))
             new_seq = False
             pattern+=1
         # Choose match closer to the end of the sequence
@@ -378,11 +425,11 @@ cdef tuple annotate(sequences, infos, verbose=False):
             message = b'No reverse primer match'
         else:
             message = b'No direct primer match'
-        final_sequence[b'error']=message
-        return False, final_sequence
+        sequences[0][b'error']=message
+        return False, sequences[0]
     
     if reversematch is None:
-        final_sequence[b'status']=b'partial'
+        sequences[0][b'status']=b'partial'
         
         if directmatch[0].forward:
             tags=(directmatch[1][3],None)
@@ -392,78 +439,86 @@ cdef tuple annotate(sequences, infos, verbose=False):
         samples = infos[None]
         
     else:
-        final_sequence[b'status']=b'full'
+        sequences[0][b'status']=b'full'
+        
+        if not not_aligned or first_match_first_seq:
+            match = sequences[0][reversematch[1][1]:reversematch[1][2]]
+        else:
+            match = sequences[1][reversematch[1][1]:reversematch[1][2]]
         
-        match = second_matched_seq[reversematch[1][1]:reversematch[1][2]]
         match = match.reverse_complement
         
-        if not not_aligned or id(second_matched_seq) == id(sequenceF):
-            final_sequence = final_sequence[0:reversematch[1][1]]
-        else:
-            cut_seq = sequenceR[reversematch[1][2]:]
+        if not not_aligned:
+            sequences[0] = sequences[0][0:reversematch[1][1]]
+        elif first_match_first_seq:
+            sequences[1] = sequences[1][reversematch[1][2]:]
             if not directmatch[0].forward:
-                cut_seq = cut_seq.reverse_complement
-            final_sequence[REVERSE_SEQ_COLUMN_NAME] = cut_seq.seq           # used by alignpairedend tool
-            final_sequence[REVERSE_QUALITY_COLUMN_NAME] = cut_seq.quality   # used by alignpairedend tool
-        
+                sequences[1] = sequences[1].reverse_complement
+            sequences[0][REVERSE_SEQUENCE_COLUMN] = sequences[1].seq           # used by alignpairedend tool
+            sequences[0][REVERSE_QUALITY_COLUMN] = sequences[1].quality   # used by alignpairedend tool
+        else:
+            sequences[0] = sequences[0][reversematch[1][2]:]
+            
         if directmatch[0].forward:
             tags=(directmatch[1][3], reversematch[1][3])
-            final_sequence[b'reverse_errors'] = reversematch[1][0]
-            final_sequence[b'reverse_primer'] = reversematch[0].raw
-            final_sequence[b'reverse_match'] = match.seq
+            sequences[0][b'reverse_errors'] = reversematch[1][0]
+            sequences[0][b'reverse_primer'] = reversematch[0].raw
+            sequences[0][b'reverse_match'] = match.seq
         
         else:
             tags=(reversematch[1][3], directmatch[1][3])
-            final_sequence[b'forward_errors'] = reversematch[1][0]
-            final_sequence[b'forward_primer'] = reversematch[0].raw
-            final_sequence[b'forward_match'] = match.seq
+            sequences[0][b'forward_errors'] = reversematch[1][0]
+            sequences[0][b'forward_primer'] = reversematch[0].raw
+            sequences[0][b'forward_match'] = match.seq
                 
         if tags[0] is not None:
-            final_sequence[b'forward_tag'] = tags[0]
+            sequences[0][b'forward_tag'] = tags[0]
         if tags[1] is not None:
-            final_sequence[b'reverse_tag'] = tags[1]
+            sequences[0][b'reverse_tag'] = tags[1]
 
         samples = infos[reversematch[3]]
         
     if not directmatch[0].forward:
-        final_sequence = final_sequence.reverse_complement
-        final_sequence[b'reversed'] = True   # used by the alignpairedend tool (in kmer_similarity.c)
+        sequences[0] = sequences[0].reverse_complement
+        sequences[0][b'reversed'] = True   # used by the alignpairedend tool (in kmer_similarity.c)
+    else:
+        sequences[0][b'reversed'] = False   # used by the alignpairedend tool (in kmer_similarity.c)
 
     sample=None
-
-    if tags[0] is not None:                                    # Direct  tag known
-        if tags[1] is not None:                                # Reverse tag known
-            sample = samples.get(tags, None)             
-        else:                                                   # Only direct tag known
-            s=[samples[x] for x in samples if x[0]==tags[0]]
-            if len(s)==1:
-                sample=s[0]
-            elif len(s)>1:
-                final_sequence[b'error']=b'multiple samples match tags'
-                return False, final_sequence
-            else:
-                sample=None
-    else: 
-        if tags[1] is not None:                                 # Only reverse tag known
-            s=[samples[x] for x in samples if x[1]==tags[1]]
-            if len(s)==1:
-                sample=s[0]
-            elif len(s)>1:
-                final_sequence[b'error']=b'multiple samples match tags'
-                return False, final_sequence
-            else:
-                sample=None
+    if not no_tags:
+        if tags[0] is not None:                                    # Direct  tag known
+            if tags[1] is not None:                                # Reverse tag known
+                sample = samples.get(tags, None)             
+            else:                                                   # Only direct tag known
+                s=[samples[x] for x in samples if x[0]==tags[0]]
+                if len(s)==1:
+                    sample=s[0]
+                elif len(s)>1:
+                    sequences[0][b'error']=b'Did not found reverse tag'
+                    return False, sequences[0]
+                else:
+                    sample=None
+        else: 
+            if tags[1] is not None:                                 # Only reverse tag known
+                s=[samples[x] for x in samples if x[1]==tags[1]]
+                if len(s)==1:
+                    sample=s[0]
+                elif len(s)>1:
+                    sequences[0][b'error']=b'Did not found forward tag'
+                    return False, sequences[0]
+                else:
+                    sample=None
+        
+        if sample is None:
+            sequences[0][b'error']=b"No sample with that tag combination"
+            return False, sequences[0]
     
-    if sample is None:
-        final_sequence[b'error']=b"Cannot assign sequence to a sample"
-        return False, final_sequence
-    
-    final_sequence.update(sample)
+        sequences[0].update(sample)
     
     if not not_aligned:
-        final_sequence[b'seq_length']=len(final_sequence)
+        sequences[0][b'seq_length']=len(sequences[0])
     
-    return True, final_sequence
+    return True, sequences[0]
 
 
 def run(config):
@@ -486,7 +541,8 @@ def run(config):
         raise Exception("Could not open input reads")
     if input[2] != View_NUC_SEQS:
         raise NotImplementedError('obi ngsfilter only works on NUC_SEQS views')
-
+    i_dms = input[0]
+    
     if "reverse" in config["ngsfilter"]:
         
         forward = input[1]        
@@ -527,8 +583,19 @@ def run(config):
     if output is None:
         raise Exception("Could not create output view")
     
+    o_dms = output[0]
+    output_0 = output[0]
     o_view = output[1]
     
+    # If stdout output, create a temporary view in the input dms that will be deleted afterwards.
+    if type(output_0)==BufferedWriter:
+        o_dms = i_dms
+        o_view_name = b"temp"
+        while o_view_name in i_dms:   # Making sure view name is unique in input DMS
+            o_view_name = o_view_name+b"_"+str2bytes(str(i))
+            i+=1
+        o_view = View_NUC_SEQS.new(i_dms, o_view_name)
+
     # Open the view containing the informations about the tags and the primers
     info_input = open_uri(config['ngsfilter']['info_view'])
     if info_input is None:
@@ -549,10 +616,19 @@ def run(config):
         unidentified = None
         
     # Initialize the progress bar
-    pb = ProgressBar(entries_len, config, seconde=5)
+    if config['obi']['noprogressbar'] == False:
+        pb = ProgressBar(entries_len, config)
+    else:
+        pb = None
 
     # Check and store primers and tags
-    infos, primer_list = read_info_view(info_view, max_errors=config['ngsfilter']['error'], verbose=False, not_aligned=not_aligned)   # TODO obi verbose option
+    try:
+        infos, primer_list = read_info_view(info_view, max_errors=config['ngsfilter']['error'], verbose=False, not_aligned=not_aligned)   # TODO obi verbose option
+    except RollbackException, e:
+        if unidentified is not None:
+            raise RollbackException("obi ngsfilter error, rollbacking views: "+str(e), o_view, unidentified)
+        else:
+            raise RollbackException("obi ngsfilter error, rollbacking view: "+str(e), o_view)
     
     aligner = Primer_search(primer_list, config['ngsfilter']['error'])
     
@@ -564,50 +640,75 @@ def run(config):
                 paired_p.revcomp.aligner = aligner
     
     if not_aligned:   # create columns used by alignpairedend tool
-        Column.new_column(o_view, REVERSE_SEQ_COLUMN_NAME, OBI_SEQ)
-        Column.new_column(o_view, REVERSE_QUALITY_COLUMN_NAME, OBI_QUAL, associated_column_name=REVERSE_SEQ_COLUMN_NAME, associated_column_version=o_view[REVERSE_SEQ_COLUMN_NAME].version)
+        Column.new_column(o_view, REVERSE_SEQUENCE_COLUMN, OBI_SEQ)
+        Column.new_column(o_view, REVERSE_QUALITY_COLUMN, OBI_QUAL, associated_column_name=REVERSE_SEQUENCE_COLUMN, associated_column_version=o_view[REVERSE_SEQUENCE_COLUMN].version)
         
-        Column.new_column(unidentified, REVERSE_SEQ_COLUMN_NAME, OBI_SEQ)
-        Column.new_column(unidentified, REVERSE_QUALITY_COLUMN_NAME, OBI_QUAL, associated_column_name=REVERSE_SEQ_COLUMN_NAME, associated_column_version=unidentified[REVERSE_SEQ_COLUMN_NAME].version)
+        if unidentified is not None:
+            Column.new_column(unidentified, REVERSE_SEQUENCE_COLUMN, OBI_SEQ)
+            Column.new_column(unidentified, REVERSE_QUALITY_COLUMN, OBI_QUAL, associated_column_name=REVERSE_SEQUENCE_COLUMN, associated_column_version=unidentified[REVERSE_SEQUENCE_COLUMN].version)
     
     g = 0
     u = 0
+    no_tags = config['ngsfilter']['notags']
     try:
         for i in range(entries_len):
             PyErr_CheckSignals()
-            pb(i)
+            if pb is not None:
+                pb(i)
             if not_aligned:
                 modseq = [Nuc_Seq.new_from_stored(forward[i]), Nuc_Seq.new_from_stored(reverse[i])]
             else:
                 modseq = [Nuc_Seq.new_from_stored(entries[i])]
-            good, oseq = annotate(modseq, infos)
+            good, oseq = annotate(modseq, infos, no_tags)
             if good:
                 o_view[g].set(oseq.id, oseq.seq, definition=oseq.definition, quality=oseq.quality, tags=oseq)
                 g+=1
             elif unidentified is not None:
-                unidentified[u].set(oseq.id, oseq.seq, definition=oseq.definition, quality=oseq.quality, tags=oseq)
+                # Untrim sequences (put original back)
+                if len(modseq) > 1:
+                    oseq[REVERSE_SEQUENCE_COLUMN] = reverse[i].seq
+                    oseq[REVERSE_QUALITY_COLUMN] = reverse[i].quality
+                    unidentified[u].set(oseq.id, forward[i].seq, definition=oseq.definition, quality=forward[i].quality, tags=oseq)
+                else:
+                    unidentified[u].set(oseq.id, entries[i].seq, definition=oseq.definition, quality=entries[i].quality, tags=oseq)
                 u+=1
     except Exception, e:
-        raise RollbackException("obi ngsfilter error, rollbacking views: "+str(e), o_view, unidentified)
+        if unidentified is not None:
+            raise RollbackException("obi ngsfilter error, rollbacking views: "+str(e), o_view, unidentified)
+        else:
+            raise RollbackException("obi ngsfilter error, rollbacking view: "+str(e), o_view)
     
-    pb(i, force=True)
-    print("", file=sys.stderr)
+    if pb is not None:
+        pb(i, force=True)
+        print("", file=sys.stderr)
 
     # Save command config in View and DMS comments
     command_line = " ".join(sys.argv[1:])
     o_view.write_config(config, "ngsfilter", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
-    unidentified.write_config(config, "ngsfilter", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
-    # Add comment about unidentified seqs
-    unidentified.comments["info"] = "View containing sequences categorized as unidentified by the ngsfilter command"
-    output[0].record_command_line(command_line)
+    if unidentified is not None:
+        unidentified.write_config(config, "ngsfilter", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
+        # Add comment about unidentified seqs
+        unidentified.comments["info"] = "View containing sequences categorized as unidentified by the ngsfilter command"
+    o_dms.record_command_line(command_line)
     
+    # stdout output: write to buffer
+    if type(output_0)==BufferedWriter:
+        logger("info", "Printing to output...")
+        o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
+        o_view.close()
+
     #print("\n\nOutput view:\n````````````", file=sys.stderr)
     #print(repr(o_view), file=sys.stderr)
 
-    input[0].close()
-    output[0].close()
-    info_input[0].close()
-    unidentified_input[0].close()
+    # If stdout output, delete the temporary result view in the input DMS
+    if type(output_0)==BufferedWriter:
+        View.delete_view(i_dms, o_view_name)
+
+    i_dms.close(force=True)
+    o_dms.close(force=True)
+    info_input[0].close(force=True)
+    if unidentified is not None:
+        unidentified_input[0].close(force=True)
     aligner.free()
 
     logger("info", "Done.")

python/obitools3/commands/sort.pyx

@@ -4,7 +4,7 @@ from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
 from obitools3.dms import DMS
 from obitools3.dms.view.view cimport View, Line_selection
 from obitools3.uri.decode import open_uri
-from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption
+from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption, addNoProgressBarOption
 from obitools3.dms.view import RollbackException
 from obitools3.apps.config import logger
 from obitools3.utils cimport str2bytes
@@ -24,6 +24,7 @@ from obitools3.dms.capi.obitypes cimport OBI_BOOL, \
 import time
 import sys
 from cpython.exc cimport PyErr_CheckSignals
+from io import BufferedWriter
 
  
 NULL_VALUE = {OBI_BOOL: OBIBool_NA, 
@@ -42,6 +43,7 @@ def addOptions(parser):
     
     addMinimalInputOption(parser)
     addMinimalOutputOption(parser)
+    addNoProgressBarOption(parser)
 
     group=parser.add_argument_group('obi sort specific options')
 
@@ -59,7 +61,7 @@ def addOptions(parser):
 
 
 def line_cmp(line, key, pb): 
-    pb   
+    pb
     if line[key] is None:
         return NULL_VALUE[line.view[key].data_type_int]
     else:
@@ -86,20 +88,28 @@ def run(config):
     if output is None:
         raise Exception("Could not create output view")
     o_dms = output[0]
-    o_view_name_final = output[1]
-    o_view_name = o_view_name_final
+    output_0 = output[0]
+    final_o_view_name = output[1]
     
-    # If the input and output DMS are not the same, create output view in input DMS first, then export it
-    # to output DMS, making sure the temporary view name is unique in the input DMS 
-    if i_dms != o_dms:
+    # If stdout output or the input and output DMS are not the same, create a temporary view that will be exported and deleted.
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
+        temporary_view_name = b"temp"
         i=0
-        while o_view_name in i_dms:
-            o_view_name = o_view_name_final+b"_"+str2bytes(str(i))
-            i+=1        
+        while temporary_view_name in i_dms:  # Making sure view name is unique in input DMS
+            temporary_view_name = temporary_view_name+b"_"+str2bytes(str(i))
+            i+=1
+        o_view_name = temporary_view_name
+        if type(output_0)==BufferedWriter:
+            o_dms = i_dms
+    else:
+        o_view_name = final_o_view_name
 
     # Initialize the progress bar
-    pb = ProgressBar(len(i_view), config, seconde=5)
-    
+    if config['obi']['noprogressbar'] == False:
+        pb = ProgressBar(len(i_view), config)
+    else:
+        pb = None
+
     keys = config['sort']['keys']
         
     selection = Line_selection(i_view)
@@ -110,10 +120,14 @@ def run(config):
     
     for k in keys:  # TODO order?
         PyErr_CheckSignals()
-        selection.sort(key=lambda line_idx: line_cmp(i_view[line_idx], k, pb(line_idx)), reverse=config['sort']['reverse'])
-
-    pb(len(i_view), force=True)
-    print("", file=sys.stderr)
+        if pb is not None:
+            selection.sort(key=lambda line_idx: line_cmp(i_view[line_idx], k, pb(line_idx)), reverse=config['sort']['reverse'])
+        else:
+            selection.sort(key=lambda line_idx: line_cmp(i_view[line_idx], k, None), reverse=config['sort']['reverse'])
+    
+    if pb is not None:
+        pb(len(i_view), force=True)
+        print("", file=sys.stderr)
 
     # Create output view with the sorted line selection
     try:
@@ -132,16 +146,23 @@ def run(config):
     # and delete the temporary view in the input DMS
     if i_dms != o_dms:
         o_view.close()
-        View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, o_view_name_final)
-        o_view = o_dms[o_view_name_final]
+        View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, final_o_view_name)
+        o_view = o_dms[final_o_view_name]
+
+    # stdout output: write to buffer
+    if type(output_0)==BufferedWriter:
+        logger("info", "Printing to output...")
+        o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
+        o_view.close()
 
     #print("\n\nOutput view:\n````````````", file=sys.stderr)
     #print(repr(o_view), file=sys.stderr)
 
-    # If the input and the output DMS are different, delete the temporary imported view used to create the final view
-    if i_dms != o_dms:
+    # If the input and the output DMS are different or if stdout output, delete the temporary imported view used to create the final view
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
         View.delete_view(i_dms, o_view_name)
-        o_dms.close()
-    i_dms.close()
+        o_dms.close(force=True)
+
+    i_dms.close(force=True)
 
     logger("info", "Done.")

python/obitools3/commands/stats.pyx

@@ -162,7 +162,7 @@ def run(config):
     lcat=0
     
     # Initialize the progress bar
-    pb = ProgressBar(len(i_view), config, seconde=5)
+    pb = ProgressBar(len(i_view), config)
     
     for i in range(len(i_view)):
         PyErr_CheckSignals()
@@ -251,7 +251,7 @@ def run(config):
     for i in range(len(sorted_stats)):
         c = sorted_stats[i][0]
         for v in c:
-            if v is not None:
+            if type(v) == bytes:
                 print(pcat % tostr(v)+"\t", end="")
             else:
                 print(pcat % str(v)+"\t", end="")
@@ -268,6 +268,6 @@ def run(config):
         print("%7d" %catcount[c], end="")
         print("%9d" %totcount[c])
 
-    input[0].close()
+    input[0].close(force=True)
     
     logger("info", "Done.")

python/obitools3/commands/tail.pyx

@@ -4,7 +4,7 @@ from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
 from obitools3.dms import DMS
 from obitools3.dms.view.view cimport View, Line_selection
 from obitools3.uri.decode import open_uri
-from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption
+from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption, addNoProgressBarOption
 from obitools3.dms.view import RollbackException
 from obitools3.apps.config import logger
 from obitools3.utils cimport str2bytes
@@ -12,6 +12,7 @@ from obitools3.utils cimport str2bytes
 import time
 import sys
 from cpython.exc cimport PyErr_CheckSignals
+from io import BufferedWriter
 
 
 __title__="Keep the N last lines of a view."
@@ -21,6 +22,7 @@ def addOptions(parser):
     
     addMinimalInputOption(parser)
     addMinimalOutputOption(parser)
+    addNoProgressBarOption(parser)
 
     group=parser.add_argument_group('obi tail specific options')
 
@@ -52,31 +54,41 @@ def run(config):
     if output is None:
         raise Exception("Could not create output view")
     o_dms = output[0]
-    o_view_name_final = output[1]
-    o_view_name = o_view_name_final
+    output_0 = output[0]
+    final_o_view_name = output[1]
     
-    # If the input and output DMS are not the same, create output view in input DMS first, then export it
-    # to output DMS, making sure the temporary view name is unique in the input DMS 
-    if i_dms != o_dms:
+    # If stdout output or the input and output DMS are not the same, create a temporary view that will be exported and deleted.
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
+        temporary_view_name = b"temp"
         i=0
-        while o_view_name in i_dms:
-            o_view_name = o_view_name_final+b"_"+str2bytes(str(i))
-            i+=1        
+        while temporary_view_name in i_dms:  # Making sure view name is unique in input DMS
+            temporary_view_name = temporary_view_name+b"_"+str2bytes(str(i))
+            i+=1
+        o_view_name = temporary_view_name
+        if type(output_0)==BufferedWriter:
+            o_dms = i_dms
+    else:
+        o_view_name = final_o_view_name
     
     start = max(len(i_view) - config['tail']['count'], 0)
 
     # Initialize the progress bar
-    pb = ProgressBar(len(i_view) - start, config, seconde=5)
+    if config['obi']['noprogressbar'] == False:
+        pb = ProgressBar(len(i_view) - start, config)
+    else:
+        pb = None
         
     selection = Line_selection(i_view)
     
     for i in range(start, len(i_view)):
         PyErr_CheckSignals()
-        pb(i)
+        if pb is not None:
+            pb(i)
         selection.append(i)
 
-    pb(i, force=True)
-    print("", file=sys.stderr)
+    if pb is not None:
+        pb(i, force=True)
+        print("", file=sys.stderr)
 
     # Save command config in View comments
     command_line = " ".join(sys.argv[1:])
@@ -97,16 +109,22 @@ def run(config):
     # and delete the temporary view in the input DMS
     if i_dms != o_dms:
         o_view.close()
-        View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, o_view_name_final)
-        o_view = o_dms[o_view_name_final]
+        View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, final_o_view_name)
+        o_view = o_dms[final_o_view_name]
+
+    # stdout output: write to buffer
+    if type(output_0)==BufferedWriter:
+        logger("info", "Printing to output...")
+        o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
+        o_view.close()
 
     #print("\n\nOutput view:\n````````````", file=sys.stderr)
     #print(repr(o_view), file=sys.stderr)
 
-    # If the input and the output DMS are different, delete the temporary imported view used to create the final view
-    if i_dms != o_dms:
+    # If the input and the output DMS are different or if stdout output, delete the temporary imported view used to create the final view
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
         View.delete_view(i_dms, o_view_name)
-        o_dms.close()
-    i_dms.close()
+        o_dms.close(force=True)
+    i_dms.close(force=True)
     
     logger("info", "Done.")

python/obitools3/commands/test.pyx

@@ -23,6 +23,7 @@ from obitools3.dms.capi.obiview cimport NUC_SEQUENCE_COLUMN, \
 import shutil
 import string
 import random
+import sys
 from cpython.exc cimport PyErr_CheckSignals
 
 
@@ -366,7 +367,7 @@ def random_new_view(config, infos, first=False):
             infos['view'] = View_NUC_SEQS.new(infos['dms'], random_unique_name(infos), comments=random_comments(config))   # TODO quality column
         else :
             infos['view'] = View.new(infos['dms'], random_unique_name(infos), comments=random_comments(config))   # TODO quality column
-        
+        infos['view'].write_config(config, "test", infos["command_line"], input_dms_name=[infos['dms'].name], input_view_name=["random"])
     print_test(config, repr(infos['view']))
     if v_to_clone is not None :
         if line_selection is None:
@@ -441,7 +442,7 @@ def addOptions(parser):
                        default=20,
                        type=int,
                        help="Maximum length of tuples. "
-                            "Default: 200")
+                            "Default: 50")
   
     group.add_argument('--max_ini_col_count','-o',
                        action="store", dest="test:maxinicolcount",
@@ -457,7 +458,7 @@ def addOptions(parser):
                        default=10000,
                        type=int,
                        help="Maximum number of lines in a column. "
-                            "Default: 10000")
+                            "Default: 1000")
  
     group.add_argument('--max_elts_per_line','-e',
                        action="store", dest="test:maxelts",
@@ -497,7 +498,8 @@ def run(config):
                                     (b"OBI_SEQ", False): random_seq, (b"OBI_SEQ", True): random_seq_tuples,
                                     (b"OBI_STR", False): random_bytes, (b"OBI_STR", True): random_bytes_tuples
                                   },
-             'tests': [test_set_and_get, test_add_col, test_delete_col, test_col_alias, test_new_view]
+             'tests': [test_set_and_get, test_add_col, test_delete_col, test_col_alias, test_new_view],
+             'command_line': " ".join(sys.argv[1:])
             }
  
     # TODO ???
@@ -529,7 +531,7 @@ def run(config):
         test_taxo(config, infos)
     
     infos['view'].close()
-    infos['dms'].close()
+    infos['dms'].close(force=True)
     shutil.rmtree(config['obi']['defaultdms']+'.obidms', ignore_errors=True)
      
     print("Done.")

python/obitools3/commands/uniq.pxd

@@ -5,5 +5,5 @@ from obitools3.dms.taxo.taxo cimport Taxonomy
 from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
 
 
-cdef merge_taxonomy_classification(View_NUC_SEQS o_view, Taxonomy taxonomy)
-cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, list mergedKeys_list=*, Taxonomy taxonomy=*, bint mergeIds=*, list categories=*, int max_elts=*)
+cdef merge_taxonomy_classification(View_NUC_SEQS o_view, Taxonomy taxonomy, dict config)
+cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, dict config, list mergedKeys_list=*, Taxonomy taxonomy=*, bint mergeIds=*, list categories=*, int max_elts=*)

python/obitools3/commands/uniq.pyx

@@ -8,22 +8,24 @@ from obitools3.dms.view import RollbackException
 from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
 from obitools3.dms.column.column cimport Column, Column_line
 from obitools3.dms.capi.obiview cimport QUALITY_COLUMN, COUNT_COLUMN, NUC_SEQUENCE_COLUMN, ID_COLUMN, TAXID_COLUMN, \
-                                        TAXID_DIST_COLUMN, MERGED_TAXID_COLUMN, MERGED_COLUMN, MERGED_PREFIX
+                                        TAXID_DIST_COLUMN, MERGED_TAXID_COLUMN, MERGED_COLUMN, MERGED_PREFIX, \
+                                        REVERSE_QUALITY_COLUMN
 from obitools3.dms.capi.obitypes cimport OBI_INT, OBI_STR, index_t
 from obitools3.apps.optiongroups import addMinimalInputOption, \
                                         addMinimalOutputOption, \
                                         addTaxonomyOption, \
-                                        addEltLimitOption
+                                        addEltLimitOption, \
+                                        addNoProgressBarOption
 from obitools3.uri.decode import open_uri
 from obitools3.apps.config import logger
-from obitools3.utils cimport tobytes, tostr
+from obitools3.utils cimport tobytes, tostr, str2bytes
 
 import sys
 from cpython.exc cimport PyErr_CheckSignals
+from io import BufferedWriter
 
 
 __title__="Group sequence records together"
- 
 
  
 def addOptions(parser):
@@ -32,6 +34,7 @@ def addOptions(parser):
     addTaxonomyOption(parser)
     addMinimalOutputOption(parser)
     addEltLimitOption(parser)
+    addNoProgressBarOption(parser)
  
     group = parser.add_argument_group('obi uniq specific options')
  
@@ -56,7 +59,7 @@ def addOptions(parser):
                              "(option can be used several times).")
 
 
-cdef merge_taxonomy_classification(View_NUC_SEQS o_view, Taxonomy taxonomy) :
+cdef merge_taxonomy_classification(View_NUC_SEQS o_view, Taxonomy taxonomy, dict config) :
     
     cdef int             taxid
     cdef Nuc_Seq_Stored  seq
@@ -69,7 +72,7 @@ cdef merge_taxonomy_classification(View_NUC_SEQS o_view, Taxonomy taxonomy) :
     cdef object          gn_sn
     cdef object          fa_sn
 
-    # Create columns
+    # Create columns and save them for efficiency
     if b"species" in o_view and o_view[b"species"].data_type_int != OBI_INT :
         o_view.delete_column(b"species")
     if b"species" not in o_view:
@@ -77,6 +80,7 @@ cdef merge_taxonomy_classification(View_NUC_SEQS o_view, Taxonomy taxonomy) :
                           b"species", 
                           OBI_INT
                          )
+    species_column = o_view[b"species"]
 
     if b"genus" in o_view and o_view[b"genus"].data_type_int != OBI_INT :
         o_view.delete_column(b"genus")
@@ -85,6 +89,7 @@ cdef merge_taxonomy_classification(View_NUC_SEQS o_view, Taxonomy taxonomy) :
                           b"genus", 
                           OBI_INT
                          )
+    genus_column = o_view[b"genus"]
 
     if b"family" in o_view and o_view[b"family"].data_type_int != OBI_INT :
         o_view.delete_column(b"family")
@@ -93,6 +98,7 @@ cdef merge_taxonomy_classification(View_NUC_SEQS o_view, Taxonomy taxonomy) :
                           b"family", 
                           OBI_INT
                          )
+    family_column = o_view[b"family"]
 
     if b"species_name" in o_view and o_view[b"species_name"].data_type_int != OBI_STR :
         o_view.delete_column(b"species_name")
@@ -101,6 +107,7 @@ cdef merge_taxonomy_classification(View_NUC_SEQS o_view, Taxonomy taxonomy) :
                           b"species_name", 
                           OBI_STR
                          )
+    species_name_column = o_view[b"species_name"]
 
     if b"genus_name" in o_view and o_view[b"genus_name"].data_type_int != OBI_STR :
         o_view.delete_column(b"genus_name")
@@ -109,6 +116,7 @@ cdef merge_taxonomy_classification(View_NUC_SEQS o_view, Taxonomy taxonomy) :
                           b"genus_name", 
                           OBI_STR
                          )
+    genus_name_column = o_view[b"genus_name"]
 
     if b"family_name" in o_view and o_view[b"family_name"].data_type_int != OBI_STR :
         o_view.delete_column(b"family_name")
@@ -117,6 +125,7 @@ cdef merge_taxonomy_classification(View_NUC_SEQS o_view, Taxonomy taxonomy) :
                           b"family_name", 
                           OBI_STR
                          )
+    family_name_column = o_view[b"family_name"]
 
     if b"rank" in o_view and o_view[b"rank"].data_type_int != OBI_STR :
         o_view.delete_column(b"rank")
@@ -125,6 +134,7 @@ cdef merge_taxonomy_classification(View_NUC_SEQS o_view, Taxonomy taxonomy) :
                           b"rank", 
                           OBI_STR
                          )
+    rank_column = o_view[b"rank"]
 
     if b"scientific_name" in o_view and o_view[b"scientific_name"].data_type_int != OBI_STR :
         o_view.delete_column(b"scientific_name")
@@ -133,9 +143,19 @@ cdef merge_taxonomy_classification(View_NUC_SEQS o_view, Taxonomy taxonomy) :
                           b"scientific_name", 
                           OBI_STR
                          )
-        
-    for seq in o_view:     
-        PyErr_CheckSignals()   
+    scientific_name_column = o_view[b"scientific_name"]  
+    
+    # Initialize the progress bar
+    if config['obi']['noprogressbar'] == False:
+        pb = ProgressBar(len(o_view), config)
+    else:
+        pb = None
+    
+    i=0
+    for seq in o_view:
+        PyErr_CheckSignals()
+        if pb is not None:
+            pb(i)
         if MERGED_TAXID_COLUMN in seq :
             m_taxids = []            
             m_taxids_dict = seq[MERGED_TAXID_COLUMN]
@@ -165,20 +185,24 @@ cdef merge_taxonomy_classification(View_NUC_SEQS o_view, Taxonomy taxonomy) :
             else:
                 fa_sn = None
                 tfa = None
-                
-            seq[b"species"] = tsp
-            seq[b"genus"] = tgn
-            seq[b"family"] = tfa
-                
-            seq[b"species_name"] = sp_sn
-            seq[b"genus_name"] = gn_sn
-            seq[b"family_name"] = fa_sn
             
-            seq[b"rank"] = taxonomy.get_rank(taxid)
-            seq[b"scientific_name"] = taxonomy.get_scientific_name(taxid)
+            species_column[i] = tsp
+            genus_column[i] = tgn
+            family_column[i] = tfa
+                
+            species_name_column[i] = sp_sn
+            genus_name_column[i] = gn_sn
+            family_name_column[i] = fa_sn
+            
+            rank_column[i] = taxonomy.get_rank(taxid)
+            scientific_name_column[i] = taxonomy.get_scientific_name(taxid)
+        i+=1
+    
+    if pb is not None:
+        pb(len(o_view), force=True)
+    
 
-
-cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, list mergedKeys_list=None, Taxonomy taxonomy=None, bint mergeIds=False, list categories=None, int max_elts=1000000) :
+cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, dict config, list mergedKeys_list=None, Taxonomy taxonomy=None, bint mergeIds=False, list categories=None, int max_elts=1000000) :
      
     cdef int            i
     cdef int            k
@@ -187,6 +211,7 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, li
     cdef int            u_idx
     cdef int            i_idx
     cdef int            i_count
+    cdef int            o_count
     cdef str            key_str
     cdef bytes          key
     cdef bytes          mkey
@@ -209,7 +234,6 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, li
     cdef Nuc_Seq_Stored i_seq
     cdef Nuc_Seq_Stored o_seq
     cdef Nuc_Seq_Stored u_seq
-    cdef Column         i_col
     cdef Column         i_seq_col
     cdef Column         i_id_col
     cdef Column         i_taxid_col
@@ -217,6 +241,8 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, li
     cdef Column         o_id_col
     cdef Column         o_taxid_dist_col
     cdef Column         o_merged_col
+    cdef Column         o_count_col
+    cdef Column         i_count_col
     cdef Column_line    i_mcol  
     cdef object         taxid_dist_dict
     cdef object         iter_view
@@ -252,7 +278,12 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, li
     mergedKeys_m = []
     for k in range(k_count):
         mergedKeys_m.append(MERGED_PREFIX + mergedKeys[k])
-     
+    
+    # Check that not trying to remerge without total count information
+    for key in mergedKeys_m:
+        if key in view and COUNT_COLUMN not in view:
+            raise Exception("\n>>>>\nError: trying to re-merge tags without total count tag. Run obi annotate to add the count tag from the relevant merged tag, i.e.: \nobi annotate --set-tag COUNT:'sum([value for key,value in sequence['MERGED_sample'].items()])' dms/input dms/output\n")
+    
     if categories is None:
         categories = []
  
@@ -274,7 +305,8 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, li
     iter_view = iter(view)
     for i_seq in iter_view :
         PyErr_CheckSignals()
-        pb(i)
+        if pb is not None:
+            pb(i)
          
         # This can't be done in the same line as the unique_id tuple creation because it generates a bug
         # where Cython (version 0.25.2) does not detect the reference to the categs_list variable and deallocates 
@@ -284,6 +316,7 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, li
         for x in categories :
             catl.append(i_seq[x])    
           
+        #unique_id = tuple(catl) + (i_seq_col[i],)
         unique_id = tuple(catl) + (i_seq_col.get_line_idx(i),)
         #unique_id = tuple(i_seq[x] for x in categories) + (seq_col.get_line_idx(i),)  # The line that cython can't read properly
          
@@ -320,7 +353,14 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, li
     for k in range(k_count):
         key = mergedKeys[k]
         merged_col_name = mergedKeys_m[k]
-        i_col = view[key]
+        
+        if merged_infos[merged_col_name]['nb_elts'] == 1:
+            raise Exception("Can't merge information from a tag with only one element (e.g. one sample ; don't use -m option)")
+        
+        if merged_col_name in view:
+            i_col = view[merged_col_name]
+        else:
+            i_col = view[key]
         
         if merged_infos[merged_col_name]['nb_elts'] > max_elts:
             str_merged_cols.append(merged_col_name)
@@ -374,23 +414,35 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, li
                           alias=MERGED_COLUMN
                          )
 
-    # Keep columns that are going to be used a lot in variables 
+    # Keep columns in variables for efficiency
     o_id_col = o_view[ID_COLUMN]
     if TAXID_DIST_COLUMN in o_view:
         o_taxid_dist_col = o_view[TAXID_DIST_COLUMN]
     if MERGED_COLUMN in o_view:
         o_merged_col = o_view[MERGED_COLUMN]
+    if COUNT_COLUMN not in o_view:
+        Column.new_column(o_view,
+                          COUNT_COLUMN,
+                          OBI_INT)
+    o_count_col = o_view[COUNT_COLUMN]
+    if COUNT_COLUMN in view:
+        i_count_col = view[COUNT_COLUMN]
+    
+    if pb is not None:
+        pb(len(view), force=True)
+        print("")
         
-    pb(len(view), force=True)
-    print("")
     logger("info", "Second browsing through the input")
+    
     # Initialize the progress bar
-    pb = ProgressBar(len(uniques), seconde=5)
+    if pb is not None:
+        pb = ProgressBar(len(view))
+        
     o_idx = 0
+    total_treated = 0
     
     for unique_id in uniques :
         PyErr_CheckSignals()
-        pb(o_idx)
         
         merged_sequences = uniques[unique_id]
         
@@ -407,7 +459,7 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, li
             merged_list = list(set(merged_list)) # deduplicate the list
             o_merged_col[o_idx] = merged_list
 
-        o_seq[COUNT_COLUMN] = 0
+        o_count = 0
 
         if TAXID_DIST_COLUMN in u_seq and i_taxid_dist_col[u_idx] is not None:
             taxid_dist_dict = i_taxid_dist_col[u_idx]
@@ -419,16 +471,20 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, li
             merged_dict[mkey] = {}
 
         for i_idx in merged_sequences:
-                        
+            PyErr_CheckSignals()
+            
+            if pb is not None:
+                pb(total_treated)
+ 
             i_id = i_id_col[i_idx]
             i_seq = view[i_idx]
 
-            if COUNT_COLUMN not in i_seq or i_seq[COUNT_COLUMN] is None:
+            if COUNT_COLUMN not in i_seq or i_count_col[i_idx] is None:
                 i_count = 1
             else:
-                i_count = i_seq[COUNT_COLUMN]
+                i_count = i_count_col[i_idx]
  
-            o_seq[COUNT_COLUMN] += i_count
+            o_count += i_count
         
             for k in range(k_count):
                                 
@@ -463,42 +519,55 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, li
                                 mcol[key2] = i_mcol[key2]
                             else:
                                 mcol[key2] = mcol[key2] + i_mcol[key2]
-            
-            # Write taxid_dist
-            if mergeIds and TAXID_COLUMN in mergedKeys:
-                if TAXID_DIST_COLUMN in str_merged_cols:
-                    o_taxid_dist_col[o_idx] = str(taxid_dist_dict)
-                else:
-                    o_taxid_dist_col[o_idx] = taxid_dist_dict
-            
-            # Write merged dicts
-            for mkey in merged_dict: 
-                if mkey in str_merged_cols:
-                    mkey_cols[mkey][o_idx] = str(merged_dict[mkey])
-                else:
-                    mkey_cols[mkey][o_idx] = merged_dict[mkey]
-                    # Sets NA values to 0  # TODO discuss, for now keep as None and test for None instead of testing for 0 in tools
-                    #for key in mkey_cols[mkey][o_idx]:
-                    #    if mkey_cols[mkey][o_idx][key] is None:
-                    #        mkey_cols[mkey][o_idx][key] = 0
-                            
+                                        
             for key in i_seq.keys():
                 # Delete informations that differ between the merged sequences
-                # TODO make special columns list?
+                # TODO make special columns list? // could be more efficient
                 if key != COUNT_COLUMN and key != ID_COLUMN and key != NUC_SEQUENCE_COLUMN and key in o_seq and o_seq[key] != i_seq[key] \
                     and key not in merged_dict :
                     o_seq[key] = None
+            
+            total_treated += 1
+            
+        # Write merged dicts
+        for mkey in merged_dict: 
+            if mkey in str_merged_cols:
+                mkey_cols[mkey][o_idx] = str(merged_dict[mkey])
+            else:
+                mkey_cols[mkey][o_idx] = merged_dict[mkey]
+                # Sets NA values to 0  # TODO discuss, for now keep as None and test for None instead of testing for 0 in tools
+                #for key in mkey_cols[mkey][o_idx]:
+                #    if mkey_cols[mkey][o_idx][key] is None:
+                #        mkey_cols[mkey][o_idx][key] = 0
 
+        # Write taxid_dist
+        if mergeIds and TAXID_COLUMN in mergedKeys:
+            if TAXID_DIST_COLUMN in str_merged_cols:
+                o_taxid_dist_col[o_idx] = str(taxid_dist_dict)
+            else:
+                o_taxid_dist_col[o_idx] = taxid_dist_dict
+                
+        o_count_col[o_idx] = o_count
         o_idx += 1
     
-    # Deletes quality column if there is one because the matching between sequence and quality will be broken (quality set to NA when sequence not)
+    if pb is not None:
+        pb(len(view), force=True)
+    
+    # Deletes quality columns if there is one because the matching between sequence and quality will be broken (quality set to NA when sequence not)
     if QUALITY_COLUMN in view:
         o_view.delete_column(QUALITY_COLUMN)
+    if REVERSE_QUALITY_COLUMN in view:
+        o_view.delete_column(REVERSE_QUALITY_COLUMN)
+    
+    # Delete old columns that are now merged
+    for k in range(k_count):
+        if mergedKeys[k] in o_view:
+            o_view.delete_column(mergedKeys[k])
     
     if taxonomy is not None:
         print("")  # TODO because in the middle of progress bar. Better solution?
         logger("info", "Merging taxonomy classification")
-        merge_taxonomy_classification(o_view, taxonomy)
+        merge_taxonomy_classification(o_view, taxonomy, config)
 
 
 
@@ -530,8 +599,23 @@ def run(config):
     if output is None:
         raise Exception("Could not create output view")
     
+    i_dms = input[0]
     entries = input[1]
-    o_view = output[1]
+    o_dms = output[0]
+    output_0 = output[0]
+    
+    # If stdout output create a temporary view that will be exported and deleted.
+    if type(output_0)==BufferedWriter:
+        temporary_view_name = b"temp"
+        i=0
+        while temporary_view_name in i_dms:  # Making sure view name is unique in input DMS
+            temporary_view_name = temporary_view_name+b"_"+str2bytes(str(i))
+            i+=1
+        o_view_name = temporary_view_name
+        o_dms = i_dms
+        o_view = View_NUC_SEQS.new(i_dms, o_view_name)
+    else:
+        o_view = output[1]
     
     if 'taxoURI' in config['obi'] and config['obi']['taxoURI'] is not None:
         taxo_uri = open_uri(config['obi']['taxoURI'])
@@ -542,15 +626,19 @@ def run(config):
         taxo = None
 
     # Initialize the progress bar
-    pb = ProgressBar(len(entries), config, seconde=5)
+    if config['obi']['noprogressbar'] == False:
+        pb = ProgressBar(len(entries), config)
+    else:
+        pb = None
     
-    try:
-        uniq_sequences(entries, o_view, pb, mergedKeys_list=config['uniq']['merge'], taxonomy=taxo, mergeIds=config['uniq']['mergeids'], categories=config['uniq']['categories'], max_elts=config['obi']['maxelts'])       
-    except Exception, e:
-        raise RollbackException("obi uniq error, rollbacking view: "+str(e), o_view)
+    if len(entries) > 0:
+        try:
+            uniq_sequences(entries, o_view, pb, config, mergedKeys_list=config['uniq']['merge'], taxonomy=taxo, mergeIds=config['uniq']['mergeids'], categories=config['uniq']['categories'], max_elts=config['obi']['maxelts'])       
+        except Exception, e:
+            raise RollbackException("obi uniq error, rollbacking view: "+str(e), o_view)
     
-    pb(len(entries), force=True)
-    print("", file=sys.stderr)
+    if pb is not None:
+        print("", file=sys.stderr)
 
     # Save command config in View and DMS comments
     command_line = " ".join(sys.argv[1:])
@@ -560,13 +648,23 @@ def run(config):
         input_dms_name.append(config['obi']['taxoURI'].split("/")[-3])
         input_view_name.append("taxonomy/"+config['obi']['taxoURI'].split("/")[-1])
     o_view.write_config(config, "uniq", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
-    output[0].record_command_line(command_line)
+    o_dms.record_command_line(command_line)
+
+    # stdout output: write to buffer
+    if type(output_0)==BufferedWriter:
+        logger("info", "Printing to output...")
+        o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
+        o_view.close()
 
     #print("\n\nOutput view:\n````````````", file=sys.stderr)
     #print(repr(o_view), file=sys.stderr)
-    
-    input[0].close()
-    output[0].close()
+
+    # If stdout output, delete the temporary result view in the input DMS
+    if type(output_0)==BufferedWriter:
+        View.delete_view(i_dms, o_view_name)
+
+    i_dms.close(force=True)
+    o_dms.close(force=True)
 
     logger("info", "Done.")
 

python/obitools3/dms/capi/obidms.pxd

@@ -34,6 +34,7 @@ cdef extern from "obidms.h" nogil:
     int obi_close_dms(OBIDMS_p dms, bint force)
     char* obi_dms_get_dms_path(OBIDMS_p dms)
     char* obi_dms_get_full_path(OBIDMS_p dms, const_char_p path_name)
+    char* obi_dms_formatted_infos(OBIDMS_p dms, bint detailed)
     void obi_close_atexit()
     
     obiversion_t obi_import_column(const char* dms_path_1, const char* dms_path_2, const char* column_name, obiversion_t version_number)

python/obitools3/dms/capi/obidmscolumn.pxd

@@ -68,3 +68,6 @@ cdef extern from "obidmscolumn.h" nogil:
     int obi_column_write_comments(OBIDMS_column_p column, const char* comments)
 
     int obi_column_add_comment(OBIDMS_column_p column, const char* key, const char* value)
+
+    char* obi_column_formatted_infos(OBIDMS_column_p column, bint detailed)
+    

python/obitools3/dms/capi/obiecopcr.pxd

@@ -23,6 +23,7 @@ cdef extern from "obi_ecopcr.h" nogil:
                    double salt_concentration,
                    int salt_correction_method,
                    int keep_nucleotides,
+                   bint keep_primers,
                    bint kingdom_mode)
 
     

python/obitools3/dms/capi/obiecotag.pxd

@@ -11,4 +11,5 @@ cdef extern from "obi_ecotag.h" nogil:
                    const char* taxonomy_name,
                    const char* output_view_name,
                    const char* output_view_comments,
-                   double ecotag_threshold)
+                   double ecotag_threshold,
+                   double bubble_threshold)

python/obitools3/dms/capi/obitaxonomy.pxd

@@ -7,6 +7,8 @@ from libc.stdint   cimport int32_t
 
 cdef extern from "obidms_taxonomy.h" nogil:
 
+    extern int MIN_LOCAL_TAXID
+    
     struct ecotxnode :
         int32_t           taxid
         int32_t           rank
@@ -18,6 +20,13 @@ cdef extern from "obidms_taxonomy.h" nogil:
     ctypedef ecotxnode ecotx_t
 
 
+    struct econame_t : # can't get this struct to be accepted by Cython ('unknown size')
+        char*      name
+        char*      class_name
+        int32_t    is_scientific_name
+        ecotxnode* taxon
+
+
     struct ecotxidx_t :   
         int32_t  count
         int32_t  max_taxid
@@ -30,9 +39,14 @@ cdef extern from "obidms_taxonomy.h" nogil:
         char**   label
 
 
+    struct econameidx_t :   
+        int32_t    count
+        econame_t* names
+
+
     struct OBIDMS_taxonomy_t :
         ecorankidx_t* ranks
-#        econameidx_t* names
+        econameidx_t* names
         ecotxidx_t*   taxa
 
     ctypedef OBIDMS_taxonomy_t* OBIDMS_taxonomy_p
@@ -51,7 +65,11 @@ cdef extern from "obidms_taxonomy.h" nogil:
     ecotx_t* obi_taxo_get_parent_at_rank(ecotx_t* taxon, int32_t rankidx)
     
     ecotx_t* obi_taxo_get_taxon_with_taxid(OBIDMS_taxonomy_p taxonomy, int32_t taxid)
+
+    char* obi_taxo_get_name_from_name_idx(OBIDMS_taxonomy_p taxonomy, int32_t idx)
     
+    ecotx_t* obi_taxo_get_taxon_from_name_idx(OBIDMS_taxonomy_p taxonomy, int32_t idx)
+
     bint obi_taxo_is_taxon_under_taxid(ecotx_t* taxon, int32_t other_taxid)
     
     ecotx_t* obi_taxo_get_species(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
@@ -71,4 +89,4 @@ cdef extern from "obidms_taxonomy.h" nogil:
     int obi_taxo_add_preferred_name_with_taxon(OBIDMS_taxonomy_p tax, ecotx_t* taxon, const char* preferred_name)
 
     const char* obi_taxo_rank_index_to_label(int32_t rank_idx, ecorankidx_t* ranks)
-    
+

python/obitools3/dms/capi/obiview.pxd

@@ -24,7 +24,10 @@ cdef extern from "obiview.h" nogil:
     extern const_char_p ID_COLUMN
     extern const_char_p DEFINITION_COLUMN
     extern const_char_p QUALITY_COLUMN
+    extern const_char_p REVERSE_QUALITY_COLUMN
+    extern const_char_p REVERSE_SEQUENCE_COLUMN
     extern const_char_p COUNT_COLUMN
+    extern const_char_p SCIENTIFIC_NAME_COLUMN
     extern const_char_p TAXID_COLUMN
     extern const_char_p MERGED_TAXID_COLUMN
     extern const_char_p MERGED_PREFIX
@@ -100,14 +103,18 @@ cdef extern from "obiview.h" nogil:
                             const_char_p comments,
                             bint create)
 
-    int obi_view_delete_column(Obiview_p view, const_char_p column_name)
-            
+    int obi_view_delete_column(Obiview_p view, const_char_p column_name, bint delete_file)
+
     OBIDMS_column_p obi_view_get_column(Obiview_p view, const_char_p column_name)
 
     OBIDMS_column_p* obi_view_get_pointer_on_column_in_view(Obiview_p view, const_char_p column_name)
 
     int obi_view_create_column_alias(Obiview_p view, const_char_p current_name, const_char_p alias)    
-    
+
+    char* obi_view_formatted_infos(Obiview_p view, bint detailed)
+
+    char* obi_view_formatted_infos_one_line(Obiview_p view)
+
     int obi_view_write_comments(Obiview_p view, const_char_p comments)
 
     int obi_view_add_comment(Obiview_p view, const_char_p key, const_char_p value)

python/obitools3/dms/column/column.pxd

@@ -22,6 +22,7 @@ cdef class Column(OBIWrapper) :
     
     cdef inline OBIDMS_column_p pointer(self)
     cdef read_elements_names(self)
+    cpdef list keys(self)
     
     @staticmethod
     cdef type get_column_class(obitype_t obitype, bint multi_elts, bint tuples)

python/obitools3/dms/column/column.pyx

@@ -14,6 +14,7 @@ from ..capi.obidms cimport obi_import_column
 from ..capi.obidmscolumn cimport OBIDMS_column_header_p, \
                                  obi_close_column, \
                                  obi_get_elements_names, \
+                                 obi_column_formatted_infos, \
                                  obi_column_write_comments
                                      
 from ..capi.obiutils cimport obi_format_date
@@ -21,7 +22,11 @@ from ..capi.obiutils cimport obi_format_date
 from ..capi.obiview cimport obi_view_add_column, \
                             obi_view_get_pointer_on_column_in_view, \
                             Obiview_p, \
-                            NUC_SEQUENCE_COLUMN
+                            NUC_SEQUENCE_COLUMN, \
+                            QUALITY_COLUMN, \
+                            REVERSE_SEQUENCE_COLUMN, \
+                            REVERSE_QUALITY_COLUMN
+
 
 from ..object cimport OBIDeactivatedInstanceError
 
@@ -34,8 +39,9 @@ from obitools3.utils cimport tobytes, \
  
 from obitools3.dms.column import typed_column
  
-from libc.stdlib  cimport free
- 
+from libc.stdlib cimport free
+from libc.string cimport strcpy
+  
 import importlib
 import inspect
 import pkgutil
@@ -92,6 +98,7 @@ cdef class Column(OBIWrapper) :
                    object    alias=b""):
         # TODO indexer_name?
         
+        cdef Column column
         cdef bytes  column_name_b = tobytes(column_name)
         cdef bytes  alias_b = tobytes(alias)
         cdef bytes  comments_b = str2bytes(json.dumps(bytes2str_object(comments)))
@@ -122,11 +129,19 @@ cdef class Column(OBIWrapper) :
         
         if data_type == OBI_QUAL:
             if associated_column_name_b == b"":
-                if NUC_SEQUENCE_COLUMN not in view:
-                     raise RuntimeError("Cannot create column %s in view %s: trying to create quality column but no NUC_SEQ column to associate it with in the view" % (bytes2str(column_name_b),
-                                                                           bytes2str(view.name)))
-                associated_column_name_b = NUC_SEQUENCE_COLUMN
-                associated_column_version = view[NUC_SEQUENCE_COLUMN].version
+                if column_name == QUALITY_COLUMN:
+                    if NUC_SEQUENCE_COLUMN not in view:
+                         raise RuntimeError("Cannot create column %s in view %s: trying to create quality column but no NUC_SEQ column to associate it with in the view" % (bytes2str(column_name_b),
+                                                                               bytes2str(view.name)))
+                    associated_column_name_b = NUC_SEQUENCE_COLUMN
+                    associated_column_version = view[NUC_SEQUENCE_COLUMN].version                    
+                elif column_name == REVERSE_QUALITY_COLUMN:
+                    if REVERSE_SEQUENCE_COLUMN not in view:
+                         raise RuntimeError("Cannot create column %s in view %s: trying to create reverse quality column but no REVERSE_SEQUENCE column to associate it with in the view" % (bytes2str(column_name_b),
+                                                                               bytes2str(view.name)))
+                    associated_column_name_b = REVERSE_SEQUENCE_COLUMN
+                    associated_column_version = view[REVERSE_SEQUENCE_COLUMN].version
+                    
         
         if (obi_view_add_column(view                      = view.pointer(),
                                 column_name               = column_name_b,
@@ -146,8 +161,19 @@ cdef class Column(OBIWrapper) :
                                 create                    = True)<0):
             raise RuntimeError("Cannot create column %s in view %s" % (bytes2str(column_name_b),
                                                                        bytes2str(view.name)))
-
-        return Column.open(view, alias_b)
+        
+        column = Column.open(view, alias_b)
+        
+        # Automatically associate nuc sequence column to quality column if necessary
+        if data_type == OBI_QUAL:
+            if column_name == QUALITY_COLUMN:
+                view[NUC_SEQUENCE_COLUMN].associated_column_name = column.name
+                view[NUC_SEQUENCE_COLUMN].associated_column_version = column.version
+            elif column_name == REVERSE_QUALITY_COLUMN:
+                view[REVERSE_SEQUENCE_COLUMN].associated_column_name = column.name
+                view[REVERSE_SEQUENCE_COLUMN].associated_column_version = column.version
+        
+        return column
  
  
     @staticmethod
@@ -276,10 +302,25 @@ cdef class Column(OBIWrapper) :
     
     @OBIWrapper.checkIsActive
     def __repr__(self) :
-        cdef bytes s
-        s = self._alias + b", data type: " + self.data_type
-        return bytes2str(s)
+        cdef str s
+        cdef char* sc
+        cdef OBIDMS_column_p pointer = self.pointer()
+        sc = obi_column_formatted_infos(pointer, False)
+        s = bytes2str(sc)
+        free(sc)
+        return s
 
+
+    @OBIWrapper.checkIsActive
+    def repr_longformat(self) :
+        cdef str s
+        cdef char* sc
+        cdef OBIDMS_column_p pointer = self.pointer()
+        sc = obi_column_formatted_infos(pointer, True)
+        s = bytes2str(sc)
+        free(sc)
+        return s
+    
          
     def close(self):  # TODO discuss, can't be called bc then bug when closing view that tries to close it in C
     
@@ -305,7 +346,10 @@ cdef class Column(OBIWrapper) :
         free(elts_names_b)
         return elts_names_list
     
-    
+    cpdef list keys(self):
+        return self._elements_names
+
+
     # Column alias property getter and setter
     @property
     def name(self):
@@ -322,7 +366,7 @@ cdef class Column(OBIWrapper) :
     @property
     def elements_names(self):
         return self._elements_names
- 
+       
     # nb_elements_per_line property getter
     @property
     def nb_elements_per_line(self):
@@ -386,6 +430,31 @@ cdef class Column(OBIWrapper) :
             raise OBIDeactivatedInstanceError()
         return obi_format_date(self.pointer().header.creation_date)
 
+
+    # associated_column name property getter and setter
+    @property
+    def associated_column_name(self):
+        if not self.active() :
+            raise OBIDeactivatedInstanceError()
+        return self.pointer().header.associated_column.column_name
+
+    @associated_column_name.setter
+    def associated_column_name(self, object new_name):
+        strcpy(self.pointer().header.associated_column.column_name, tobytes(new_name))
+
+
+    # associated_column version property getter and setter
+    @property
+    def associated_column_version(self):
+        if not self.active() :
+            raise OBIDeactivatedInstanceError()
+        return self.pointer().header.associated_column.version
+
+    @associated_column_version.setter
+    def associated_column_version(self, int new_version):
+        self.pointer().header.associated_column.version = new_version
+
+
     # comments property getter
     @property
     def comments(self):

python/obitools3/dms/dms.pyx

@@ -10,7 +10,8 @@ from .capi.obidms cimport obi_open_dms, \
                           obi_dms_exists, \
                           obi_dms_get_full_path, \
                           obi_close_atexit, \
-                          obi_dms_write_comments
+                          obi_dms_write_comments, \
+                          obi_dms_formatted_infos
                                                       
 from .capi.obitypes cimport const_char_p
                             
@@ -32,6 +33,8 @@ from .object import OBIWrapper
 import json
 import time
 
+from libc.stdlib cimport free
+
 
 cdef class DMS(OBIWrapper):    
     
@@ -94,16 +97,16 @@ cdef class DMS(OBIWrapper):
         return dms
     
     
-    def close(self) :
+    def close(self, force=False) :
         '''
-        Closes the DMS instance and free the associated memory
+        Closes the DMS instance and free the associated memory (no counter, closing is final)
         
         The `close` method is automatically called by the object destructor.
         '''
         cdef OBIDMS_p pointer = self.pointer()
         if self.active() :
             OBIWrapper.close(self)
-            if (obi_close_dms(pointer, False)) < 0 :
+            if (obi_close_dms(pointer, force=force)) < 0 :
                 raise Exception("Problem closing an OBIDMS")
 
 
@@ -223,11 +226,24 @@ cdef class DMS(OBIWrapper):
 
 
     @OBIWrapper.checkIsActive
-    def __repr__(self):
-        cdef str s 
-        s=""
-        for view_name in self.keys():
-            s = s + repr(self.get_view(view_name)) + "\n"
+    def __repr__(self) :
+        cdef str s
+        cdef char* sc
+        cdef OBIDMS_p pointer = self.pointer()
+        sc = obi_dms_formatted_infos(pointer, False)
+        s = bytes2str(sc)
+        free(sc)
+        return s
+
+
+    @OBIWrapper.checkIsActive
+    def repr_longformat(self) :
+        cdef str s
+        cdef char* sc
+        cdef OBIDMS_p pointer = self.pointer()
+        sc = obi_dms_formatted_infos(pointer, True)
+        s = bytes2str(sc)
+        free(sc)
         return s
     
 
@@ -254,12 +270,13 @@ cdef class DMS(OBIWrapper):
     # bash command history property getter
     @property
     def bash_history(self):
-        s = b"#!/bin/bash\n\n"
+        #s = b"#!${bash}/bin/bash\n\n"
+        s = b""
         first = True
         for command in self.command_line_history:
             s+=b"#"
             s+=command[b"time"]
-            s+=b"\n"
+            s+=b"\nobi "
             s+=command[b"command"]
             s+=b"\n"
         return s

python/obitools3/dms/obiseq.pxd

@@ -39,4 +39,6 @@ cdef class Nuc_Seq_Stored(Seq_Stored) :
     cpdef set_quality_char(self, object new_qual, int offset=*)
     cpdef object build_quality_array(self, list quality)
     cpdef bytes build_reverse_complement(self)
-    cpdef str get_str(self)
+    cpdef str get_str(self)
+    cpdef repr_bytes(self)
+    

python/obitools3/dms/obiseq.pyx

@@ -431,9 +431,12 @@ cdef class Nuc_Seq_Stored(Seq_Stored) :
         return len(self._view.get_column(NUC_SEQUENCE_COLUMN).get_line(self.index))
 
     def __repr__(self):
+        return bytes2str(self.repr_bytes())
+    
+    cpdef repr_bytes(self):
         if self.quality is None:
             formatter = FastaFormat()
         else:
             formatter = FastqFormat()
-        return bytes2str(formatter(self))
+        return formatter(self)
 

python/obitools3/dms/taxo/taxo.pxd

@@ -11,11 +11,14 @@ cdef class Taxonomy(OBIWrapper) :
     cdef bytes  _name
     cdef DMS    _dms
     cdef list   _ranks
+    cdef dict   _name_dict
     
     cdef inline OBIDMS_taxonomy_p pointer(self)
+    cdef fill_name_dict(self)
 
     cpdef Taxon get_taxon_by_idx(self, int idx)
     cpdef Taxon get_taxon_by_taxid(self, int taxid)
+    cpdef Taxon get_taxon_by_name(self, object taxon_name, object restricting_taxid=*)
     cpdef write(self, object prefix)
     cpdef int add_taxon(self, str name, str rank_name, int parent_taxid, int min_taxid=*)
     cpdef object get_species(self, int taxid)

python/obitools3/dms/taxo/taxo.pyx

@@ -15,7 +15,11 @@ from ..capi.obitaxonomy cimport obi_taxonomy_exists, \
                                 obi_taxo_get_species, \
                                 obi_taxo_get_genus, \
                                 obi_taxo_get_family, \
-                                ecotx_t                
+                                ecotx_t, \
+                                econame_t, \
+                                obi_taxo_get_name_from_name_idx, \
+                                obi_taxo_get_taxon_from_name_idx
+                                
                                            
 from cpython.pycapsule cimport PyCapsule_New, PyCapsule_GetPointer
 import tarfile
@@ -24,11 +28,29 @@ from libc.stdlib  cimport free
 
 
 cdef class Taxonomy(OBIWrapper) :
-    # TODO function to import taxonomy?
-    
+    # TODO function to import taxonomy?    
+     
     cdef inline OBIDMS_taxonomy_p pointer(self) :
         return <OBIDMS_taxonomy_p>(self._pointer)        
 
+    cdef fill_name_dict(self):
+        print("Indexing taxon names...")
+        
+        cdef OBIDMS_taxonomy_p pointer = self.pointer()
+        cdef ecotx_t*     taxon_p
+        cdef object       taxon_capsule
+        cdef bytes        name
+        cdef int          count
+        cdef int          n
+        
+        count = (<OBIDMS_taxonomy_p>pointer).names.count
+        
+        for n in range(count) :
+            name = obi_taxo_get_name_from_name_idx(pointer, n)
+            taxon_p = obi_taxo_get_taxon_from_name_idx(pointer, n)
+            taxon_capsule = PyCapsule_New(taxon_p, NULL, NULL)
+            self._name_dict[name] = Taxon(taxon_capsule, self)
+
 
     @staticmethod
     def exists(DMS dms, object name) :
@@ -75,7 +97,8 @@ cdef class Taxonomy(OBIWrapper) :
 
         taxo._dms = dms
         taxo._name = tobytes(name)
-        
+        taxo._name_dict = {}
+        taxo.fill_name_dict()
         taxo._ranks = []
         for r in range((<OBIDMS_taxonomy_p>pointer).ranks.count) :
             taxo._ranks.append(obi_taxo_rank_index_to_label(r, (<OBIDMS_taxonomy_p>pointer).ranks))
@@ -118,7 +141,8 @@ cdef class Taxonomy(OBIWrapper) :
 
         taxo._dms = dms
         taxo._name = folder_path
-        
+        taxo._name_dict = {}
+        taxo.fill_name_dict()
         taxo._ranks = []
         for r in range((<OBIDMS_taxonomy_p>pointer).ranks.count) :
             taxo._ranks.append(obi_taxo_rank_index_to_label(r, (<OBIDMS_taxonomy_p>pointer).ranks))
@@ -129,8 +153,8 @@ cdef class Taxonomy(OBIWrapper) :
     def __getitem__(self, object ref):     
         if type(ref) == int :
             return self.get_taxon_by_taxid(ref)
-        else :
-            raise NotImplementedError()
+        elif type(ref) == str or type(ref) == bytes :
+            return self.get_taxon_by_name(ref)
 
 
     cpdef Taxon get_taxon_by_taxid(self, int taxid):
@@ -143,6 +167,19 @@ cdef class Taxonomy(OBIWrapper) :
         return Taxon(taxon_capsule, self)
 
 
+    cpdef Taxon get_taxon_by_name(self, object taxon_name, object restricting_taxid=None):            
+        taxon = self._name_dict.get(tobytes(taxon_name), None)
+        if not taxon:
+            return None
+        elif restricting_taxid:
+            if self.is_ancestor(restricting_taxid, taxon.taxid):
+                return taxon
+            else:
+                return None
+        else:
+            return taxon
+
+
     cpdef Taxon get_taxon_by_idx(self, int idx):
         cdef ecotx_t* taxa
         cdef ecotx_t* taxon_p
@@ -232,7 +269,7 @@ cdef class Taxonomy(OBIWrapper) :
  
         taxa = self.pointer().taxa.taxon
  
-        # Yield each taxid
+        # Yield each taxon
         for t in range(self.pointer().taxa.count):
             taxon_p = <ecotx_t*> (taxa+t)
             taxon_capsule = PyCapsule_New(taxon_p, NULL, NULL)

python/obitools3/dms/view/view.pxd

@@ -20,9 +20,14 @@ cdef class View(OBIWrapper):
     cdef DMS _dms
     
     cdef inline Obiview_p pointer(self)   
+
+    cpdef print_to_output(self, 
+                          object output, 
+                          bint noprogressbar=*)
         
     cpdef delete_column(self, 
-                        object column_name)
+                        object column_name,
+                        bint delete_file=*)
     
     cpdef rename_column(self, 
                         object current_name, 
@@ -60,6 +65,8 @@ cdef class Line :
     cdef index_t _index
     cdef View    _view
     
+    cpdef repr_bytes(self)
+
 
 cdef register_view_class(bytes view_type_name,
                          type view_class)

python/obitools3/dms/view/view.pyx

@@ -6,6 +6,9 @@ cdef dict __VIEW_CLASS__= {}
 
 from libc.stdlib  cimport malloc
 
+from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
+from obitools3.version import version
+
 from ..capi.obiview cimport Alias_column_pair_p, \
                             obi_new_view, \
                             obi_open_view, \
@@ -16,7 +19,9 @@ from ..capi.obiview cimport Alias_column_pair_p, \
                             obi_view_delete_column, \
                             obi_view_create_column_alias, \
                             obi_view_write_comments, \
-                            obi_delete_view
+                            obi_delete_view, \
+                            obi_view_formatted_infos, \
+                            obi_view_formatted_infos_one_line
                            
 from ..capi.obidmscolumn cimport OBIDMS_column_p
 from ..capi.obidms cimport OBIDMS_p
@@ -48,10 +53,15 @@ from ..capi.obidms cimport obi_import_view
 
 from obitools3.format.tab import TabFormat
 
+from cpython.exc cimport PyErr_CheckSignals
+
 import importlib
 import inspect
 import pkgutil
 import json
+import sys
+
+from libc.stdlib cimport free
 
 
 cdef class View(OBIWrapper) :
@@ -178,13 +188,50 @@ cdef class View(OBIWrapper) :
     
     
     @OBIWrapper.checkIsActive
-    def __repr__(self) :         
-        cdef str s = "#View name:\n{name:s}\n#Line count:\n{line_count:d}\n#Columns:\n".format(name       = bytes2str(self.name),
-                                                                                                                         line_count = self.line_count)
-        for column_name in self.keys() :
-            s = s + repr(self[column_name]) + '\n'
+    def __repr__(self) :
+        cdef str s
+        cdef char* sc
+        cdef Obiview_p pointer = self.pointer()
+        sc = obi_view_formatted_infos(pointer, False)
+        s = bytes2str(sc)
+        free(sc)
         return s
-    
+
+
+    @OBIWrapper.checkIsActive
+    def repr_longformat(self) :
+        cdef str s
+        cdef char* sc
+        cdef Obiview_p pointer = self.pointer()
+        sc = obi_view_formatted_infos(pointer, True)
+        s = bytes2str(sc)
+        free(sc)
+        return s
+
+
+    cpdef print_to_output(self, object output, bint noprogressbar=False):      
+        
+        cdef int i
+        cdef Line entry
+        
+        self.checkIsActive(self)
+        
+        # Initialize the progress bar
+        if noprogressbar == False:
+            pb = ProgressBar(len(self))
+        else:
+            pb = None
+        i=0
+        for entry in self:
+            PyErr_CheckSignals()
+            if pb is not None:
+                pb(i)
+            output.write(entry.repr_bytes()+b"\n")
+            i+=1
+        if pb is not None:
+            pb(len(self), force=True)
+            print("", file=sys.stderr)
+
      
     def keys(self):
         
@@ -227,7 +274,8 @@ cdef class View(OBIWrapper) :
 
     
     cpdef delete_column(self, 
-                        object column_name) :
+                        object column_name,
+                        bint delete_file=False) :
 
         cdef bytes column_name_b = tobytes(column_name)
 
@@ -239,7 +287,7 @@ cdef class View(OBIWrapper) :
         col.close()
         
         # Remove the column from the view which closes the C structure
-        if obi_view_delete_column(self.pointer(), column_name_b) < 0 :
+        if obi_view_delete_column(self.pointer(), column_name_b, delete_file) < 0 :
             raise RollbackException("Problem deleting column %s from a view",
                             bytes2str(column_name_b), self)
 
@@ -297,11 +345,17 @@ cdef class View(OBIWrapper) :
                                        nb_elements_per_line=new_nb_elements_per_line, elements_names=new_elements_names, 
                                        comments=old_column.comments, alias=column_name_b+tobytes('___new___'))
         
+        switch_to_dict = old_column.nb_elements_per_line == 1 and new_nb_elements_per_line > 1
+        ori_key = old_column._elements_names[0]
+        
         for i in range(length) :
-            new_column[i] = old_column[i]
+            if switch_to_dict :
+                new_column[i] = {ori_key: old_column[i]}
+            else:
+                new_column[i] = old_column[i]
 
         # Remove old column from view
-        self.delete_column(column_name_b)
+        self.delete_column(column_name_b, delete_file=True)
 
         # Rename new
         new_column.name = column_name_b
@@ -398,6 +452,7 @@ cdef class View(OBIWrapper) :
             for i in range(len(input_view_name)):
                 input_str.append(tostr(input_dms_name[i])+"/"+tostr(input_view_name[i]))
         comments["input_str"] = input_str
+        comments["version"] = version
         return bytes2str_object(comments)
 
     
@@ -519,11 +574,12 @@ cdef class View(OBIWrapper) :
     # bash command history property getter
     @property
     def bash_history(self):
-        s = b"#!/bin/bash\n\n"
+        s = b""
         first = True
         for level in self.view_history:
             command_list = [level[input][b"command_line"] for input in level.keys()]
             for command in command_list:
+                s+=b"obi "
                 s+=command
                 s+=b"\n"
         return s
@@ -749,8 +805,12 @@ cdef class Line :
 
 
     def __repr__(self):
+        return bytes2str(self).repr_bytes()
+
+
+    cpdef repr_bytes(self):
         formatter = TabFormat(header=False)
-        return bytes2str(formatter(self))
+        return formatter(self)
 
 
     # View property getter

python/obitools3/format/tab.pyx

@@ -3,8 +3,9 @@
 cimport cython
 from obitools3.dms.view.view cimport Line
 from obitools3.utils cimport bytes2str_object, str2bytes, tobytes
-from obitools3.dms.column.column cimport Column_line
+from obitools3.dms.column.column cimport Column_line, Column_multi_elts
 
+import sys
 
 cdef class TabFormat:
     
@@ -25,19 +26,33 @@ cdef class TabFormat:
         for k in self.tags:
             
             if self.header and self.first_line:
-                value = tobytes(k)
+                if isinstance(data.view[k], Column_multi_elts):
+                    keys = data.view[k].keys()
+                    keys.sort()
+                    for k2 in keys:
+                        line.append(tobytes(k)+b':'+tobytes(k2))
+                else:
+                    line.append(tobytes(k))
             else:
                 value = data[k]
-                if value is not None:
-                    if type(value) == Column_line:
-                        value = value.bytes()
+                if isinstance(data.view[k], Column_multi_elts):
+                    keys = data.view[k].keys()
+                    keys.sort()
+                    if value is None:  # all keys at None
+                        for k2 in keys: # TODO could be much more efficient
+                            line.append(self.NAString)
                     else:
-                        value = str2bytes(str(bytes2str_object(value))) # genius programming
-                if value is None:
-                    value = self.NAString
-            
-            line.append(value)
-      	
+                        for k2 in keys: # TODO could be much more efficient
+                            if value[k2] is not None:
+                                line.append(str2bytes(str(bytes2str_object(value[k2]))))  # genius programming
+                            else:
+                                line.append(self.NAString)
+                else:
+                    if value is not None:
+                        line.append(str2bytes(str(bytes2str_object(value))))
+                    else:
+                        line.append(self.NAString)
+                  	
         if self.first_line:
             self.first_line = False
       		

python/obitools3/libalign/_solexapairend.pyx

@@ -6,6 +6,7 @@ from .solexapairend import iterOnAligment
 from .shifted_ali cimport Ali_shifted
 
 from obitools3.dms.capi.obiview cimport Obiview_p, QUALITY_COLUMN, NUC_SEQUENCE_COLUMN, \
+                                        REVERSE_SEQUENCE_COLUMN, REVERSE_QUALITY_COLUMN, \
                                         obi_set_qual_int_with_elt_idx_and_col_p_in_view, \
                                         obi_set_str_with_elt_idx_and_col_p_in_view
                                         
@@ -13,7 +14,6 @@ from obitools3.dms.capi.obidmscolumn cimport OBIDMS_column_p
 
 from obitools3.dms.view.view cimport View
 from obitools3.dms.column.column cimport Column
-from obitools3.commands.ngsfilter import REVERSE_SEQ_COLUMN_NAME, REVERSE_QUALITY_COLUMN_NAME
 
 from math import log10
 
@@ -183,12 +183,13 @@ def buildConsensus(ali, seq, ref_tags=None):
         # doesn't work because uint8_t* are forced into bytes by cython (nothing read/kept beyond 0 values)
         #obi_set_qual_int_with_elt_idx_and_col_p_in_view(view_p, col_p, seq.index, 0, ali.consensus_qual, ali.consensus_len)
         seq.set(ref_tags.id+b"_CONS", ali.consensus_seq, quality=ali.consensus_qual)
-        seq[b'ali_length'] = ali.consensus_len
-        seq[b'score_norm']=float(ali.score)/ali.consensus_len
+        seq[b"seq_length"] = ali.consensus_len
+        seq[b"overlap_length"] = ali.overlap_len
+        seq[b'score_norm']=round(float(ali.score)/ali.overlap_len, 3)
         seq[b'shift']=ali.shift
     else:
         if len(ali[0])>999:   # TODO why?
-            raise AssertionError,"Too long alignemnt"
+            raise AssertionError,"Too long alignment"
     
         ic=IterOnConsensus(ali)
     
@@ -233,7 +234,7 @@ def buildConsensus(ali, seq, ref_tags=None):
     seq[b'mode']=b'alignment'
 
     for tag in ref_tags:
-        if tag != REVERSE_SEQ_COLUMN_NAME and tag != REVERSE_QUALITY_COLUMN_NAME and \
+        if tag != REVERSE_SEQUENCE_COLUMN and tag != REVERSE_QUALITY_COLUMN and \
             tag != NUC_SEQUENCE_COLUMN and tag != QUALITY_COLUMN:
             seq[tag] = ref_tags[tag]
 
@@ -250,11 +251,22 @@ def buildJoinedSequence(ali, reverse, seq, forward=None):
     quality.extend(reverse.quality)
     seq.set(forward.id +b"_PairedEnd", s, definition=forward.definition, quality=quality)
     seq[b"score"]=ali.score
-    seq[b"ali_direction"]=ali.direction
+    if len(ali.direction) > 0:
+        seq[b"ali_direction"]=ali.direction
+    else:
+        seq[b"ali_direction"]=None
     seq[b"mode"]=b"joined"
-    seq[b"pairedend_limit"]=len(forward)    
+    seq[b"pairedend_limit"]=len(forward)
+    seq[b"seq_length"] = ali.consensus_len
+    seq[b"overlap_length"] = ali.overlap_len
+    if ali.overlap_len > 0:
+        seq[b'score_norm']=round(float(ali.score)/ali.overlap_len, 3)
+    else:
+        seq[b"score_norm"]=0.0
+  
     for tag in forward:
-        if tag != REVERSE_SEQ_COLUMN_NAME and tag != REVERSE_QUALITY_COLUMN_NAME:
+        if tag != REVERSE_SEQUENCE_COLUMN and tag != REVERSE_QUALITY_COLUMN and \
+            tag != NUC_SEQUENCE_COLUMN and tag != QUALITY_COLUMN:
             seq[tag] = forward[tag]
     return seq
 

python/obitools3/parsers/embl.pyx

@@ -156,6 +156,9 @@ def emblIterator_file(lineiterator,
         yield seq
         read+=1
     
+    # Last sequence
+    seq = emblParser(entry)
+        
     yield seq
     
     free(entry)
@@ -174,7 +177,7 @@ def emblIterator_dir(dir_path,
     for filename in files:
         if read==only:
             return
-        print("Parsing file %s (%d/%d)" % (tostr(filename), read_files, len(files)))
+        print("Parsing file %s (%d/%d)" % (tostr(filename), read_files+1, len(files)))
         f = uopen(filename)
         if only is not None:
             only_f = only-read

python/obitools3/parsers/fasta.pyx

@@ -104,6 +104,7 @@ def fastaNucIterator(lineiterator,
     cdef bytes      sequence
     cdef int        skipped, ionly, read
     cdef Nuc_Seq    seq
+    cdef bint       stop
     
     if only is None:
         ionly = -1
@@ -130,7 +131,8 @@ def fastaNucIterator(lineiterator,
     else:
         line = firstline       
     
-    while True:
+    stop=False
+    while not stop:
                 
         if ionly >= 0 and read >= ionly:
             break
@@ -153,7 +155,7 @@ def fastaNucIterator(lineiterator,
                 s.append(line[0:-1])
                 line = next(iterator)
         except StopIteration:
-            pass
+            stop=True
         
         sequence  = b"".join(s)        
         

python/obitools3/parsers/genbank.pyx

@@ -25,8 +25,9 @@ from libc.string cimport strcpy, strlen
 _featureMatcher = re.compile(b'^FEATURES.+\n(?=ORIGIN)',re.DOTALL + re.M)
 
 _headerMatcher = re.compile(b'^LOCUS.+(?=\nFEATURES)', re.DOTALL + re.M)
-_seqMatcher    = re.compile(b'(?<=ORIGIN).+(?=//\n)', re.DOTALL + re.M)
-_cleanSeq      = re.compile(b'[ \n0-9]+')
+_seqMatcher    = re.compile(b'ORIGIN.+(?=//\n)', re.DOTALL + re.M)
+_cleanSeq1     = re.compile(b'ORIGIN.+\n')
+_cleanSeq2     = re.compile(b'[ \n0-9]+')
 _acMatcher     = re.compile(b'(?<=^ACCESSION   ).+',re.M)
 _deMatcher     = re.compile(b'(?<=^DEFINITION  ).+\n( .+\n)*',re.M)
 _cleanDe       = re.compile(b'\n *')
@@ -42,7 +43,8 @@ def genbankParser(bytes text):
         ft     = _featureMatcher.search(text).group()
         
         s      = _seqMatcher.search(text).group()
-        s      = _cleanSeq.sub(b'', s).upper()
+        s      = _cleanSeq1.sub(b'', s)
+        s      = _cleanSeq2.sub(b'', s)
         
         acs    = _acMatcher.search(text).group()
         acs    = acs.split()
@@ -51,23 +53,23 @@ def genbankParser(bytes text):
         
         de     = _deMatcher.search(header).group()
         de     = _cleanDe.sub(b' ',de).strip().strip(b'.')
-
+    
+        tags = {}
+        extractTaxon(ft, tags)
+            
+        seq = Nuc_Seq(ac,
+                      s,
+                      definition=de,
+                      quality=None,
+                      offset=-1,
+                      tags=tags)
+    
     except Exception as e:
         print("\nCould not import sequence id:", text.split()[1], "(error raised:", e, ")")
         # Do not raise any Exception if you need the possibility to resume the generator
         # (Python generators can't resume after any exception is raised)
         return None
-    
-    tags = {}
-    extractTaxon(ft, tags)
-        
-    seq = Nuc_Seq(ac,
-                  s,
-                  definition=de,
-                  quality=None,
-                  offset=-1,
-                  tags=tags)
-    
+
     return seq
 
 
@@ -153,6 +155,9 @@ def genbankIterator_file(lineiterator,
         yield seq
         read+=1
     
+    # Last sequence
+    seq = genbankParser(entry)
+    
     yield seq
     
     free(entry)
@@ -168,10 +173,12 @@ def genbankIterator_dir(dir_path,
     read = 0
     read_files = 0
     files = [filename for filename in glob.glob(os.path.join(path, b'*.gbff*'))]
+    files.extend([filename for filename in glob.glob(os.path.join(path, b'*.seq*'))])  # new genbank extension
+    files = list(set(files))
     for filename in files:
         if read==only:
             return
-        print("Parsing file %s (%d/%d)" % (tostr(filename), read_files, len(files)))
+        print("Parsing file %s (%d/%d)" % (tostr(filename), read_files+1, len(files)))
         f = uopen(filename)
         if only is not None:
             only_f = only-read

python/obitools3/parsers/ngsfilter.pyx

@@ -57,6 +57,9 @@ def ngsfilterIterator(lineiterator,
         split_line = line.split()
         tags = split_line.pop(2)
         tags = tags.split(b":")
+        for t_idx in range(len(tags)):
+            if tags[t_idx]==b"-" or tags[t_idx]==b"None" or tags[t_idx]==b"":
+                tags[t_idx] = nastring
         if len(tags) == 1:          # Forward and reverse tags are the same
             tags.append(tags[0])
         split_line.insert(2, tags[0])

python/obitools3/uri/decode.pyx

@@ -171,7 +171,8 @@ Reads an URI and returns a tuple containing:
 def open_uri(uri,
              bint input=True,
              type newviewtype=View,
-             dms_only=False):
+             dms_only=False,
+             force_file=False):
     
     cdef bytes urib = tobytes(uri)
     cdef bytes scheme
@@ -195,9 +196,9 @@ def open_uri(uri,
     if 'obi' not in config:
         config['obi']={}
     
-    try:
+    if not force_file and "defaultdms" in config["obi"]:
         default_dms=config["obi"]["defaultdms"]
-    except KeyError:
+    else:
         default_dms=None
         
     try:
@@ -209,10 +210,11 @@ def open_uri(uri,
     
     error = None
     
-    if scheme==b"dms" or \
-        (scheme==b"" and \
-         (((not input) and "outputformat" not in config["obi"]) or \
-         (input and "inputformat" not in config["obi"]))):   # TODO maybe not best way
+    if urib != b"-" and \
+        (scheme==b"dms" or \
+         (scheme==b"" and \
+          (((not input) and "outputformat" not in config["obi"]) or \
+          (input and "inputformat" not in config["obi"])))):   # TODO maybe not best way
         
         if default_dms is not None and b"/" not in urip.path:   # assuming view to open in default DMS (TODO discuss)
             dms=(default_dms, urip.path)
@@ -274,11 +276,11 @@ def open_uri(uri,
             iseq = urib
             objclass = bytes
     else:  # TODO update uopen to be able to write? 
-        if urip.path:
-            file = open(urip.path, 'wb')
-        else:
+        if not urip.path or urip.path == b'-':
             file = sys.stdout.buffer
-        
+        else:
+            file = open(urip.path, 'wb')
+
     if file is not None:
         qualifiers=parse_qs(urip.query)
         
@@ -462,7 +464,7 @@ def open_uri(uri,
         if format is not None:
             if seqtype==b"nuc":
                 objclass = Nuc_Seq    # Nuc_Seq_Stored? TODO
-                if format==b"fasta":
+                if format==b"fasta" or format==b"silva":
                     if input:
                         iseq = fastaNucIterator(file, 
                                                 skip=skip, 

python/obitools3/utils.pxd

@@ -2,7 +2,7 @@
 
 from obitools3.dms.capi.obitypes cimport obitype_t, index_t
 
-cpdef bytes format_separator(bytes format)
+cpdef bytes format_uniq_pattern(bytes format)
 cpdef int count_entries(file, bytes format)
 
 cdef obi_errno_to_exception(index_t line_nb=*, object elt_id=*, str error_message=*)

python/obitools3/utils.pyx

@@ -24,11 +24,11 @@ import glob
 import gzip
 
 
-cpdef bytes format_separator(bytes format):
+cpdef bytes format_uniq_pattern(bytes format):
     if format == b"fasta":
         return b"\n>"
     elif format == b"fastq":
-        return b"\n@"
+        return b"\n\+\n"
     elif format == b"ngsfilter" or format == b"tabular":
         return b"\n"
     elif format == b"genbank" or format == b"embl":
@@ -42,7 +42,7 @@ cpdef bytes format_separator(bytes format):
 cpdef int count_entries(file, bytes format):
     
     try:
-        sep = format_separator(format)
+        sep = format_uniq_pattern(format)
         if sep is None:
             return -1
         sep = re.compile(sep)
@@ -72,7 +72,7 @@ cpdef int count_entries(file, bytes format):
                 return -1
             mmapped_file = mmap.mmap(f.fileno(), 0, access=mmap.ACCESS_READ)
             total_count += len(re.findall(sep, mmapped_file))
-            if format != b"ngsfilter" and format != b"tabular":
+            if format != b"ngsfilter" and format != b"tabular" and format != b"embl" and format != b"genbank" and format != b"fastq":
                 total_count += 1 # adding +1 for 1st entry because separators include \n (ngsfilter and tabular already count one more because of last \n)
             
     except:
@@ -166,7 +166,9 @@ cdef object bytes2str_object(object value):  # Only works if complex types are d
                     value[k] = bytes2str(v)
             if type(k) == bytes:
                 value[bytes2str(k)] = value.pop(k)
-    elif isinstance(value, list):
+    elif isinstance(value, list) or isinstance(value, tuple):
+        if isinstance(value, tuple):
+            value = list(value)
         for i in range(len(value)):
             if isinstance(value[i], list) or isinstance(value[i], dict):
                 value[i] = bytes2str_object(value[i])

python/obitools3/version.py

@@ -1,5 +1,5 @@
 major = 3
 minor = 0
-serial= '0-beta1'
+serial= '0b37'
 
-version ="%d.%02d.%s" % (major,minor,serial)
+version ="%d.%d.%s" % (major,minor,serial)

requirements.txt

@@ -0,0 +1,5 @@
+--extra-index-url https://pypi.python.org/simple/
+Cython>=0.24
+Sphinx>=1.2.0
+ipython>=3.0.0
+breathe>=4.0.0

setup.py

@@ -5,8 +5,9 @@ import re
 import subprocess
 
 from distutils import log
-from distutils.core import setup
-    
+#from distutils.core import setup
+from setuptools import setup    # to work with pip
+
 from distutils.core import Extension
 from distutils.sysconfig import get_python_lib
 
@@ -16,6 +17,8 @@ from distutils.extension import Extension
 
 from distutils.dist import Distribution as ori_Distribution
 
+from python.obitools3.version import version
+
 
 class Distribution(ori_Distribution):
     
@@ -24,10 +27,11 @@ class Distribution(ori_Distribution):
         
         ori_Distribution.__init__(self, attrs)
         
-        self.global_options.insert(0,('cobitools3', None, "intall location of the C library"
+        self.global_options.insert(0,('cobitools3', None, "install location of the C library"
                                      ))
 
 from distutils.command.build import build as build_ori
+from setuptools.command.bdist_egg import bdist_egg as bdist_egg_ori
 from distutils.core import Command
 
 
@@ -68,6 +72,12 @@ class build(build_ori):
         build_ori.run(self)
 
 
+class bdist_egg(bdist_egg_ori):
+    def run(self):
+        self.run_command('build_clib')
+        bdist_egg_ori.run(self)
+
+
 sys.path.append(os.path.abspath("python"))
 
 
@@ -83,12 +93,13 @@ def findPackage(root,base=None):
   
 
 PACKAGE     = "OBITools3"
-VERSION     = "3.0.0-beta1"
+VERSION     = version
 AUTHOR      = 'Celine Mercier'
 EMAIL       = 'celine.mercier@metabarcoding.org'
-URL         = "http://metabarcoding.org/obitools3"
+URL         = "https://metabarcoding.org/obitools3"
+PLATFORMS   = "posix"
 LICENSE     = "CeCILL-V2"
-DESCRIPTION = "Tools and library for DNA metabarcoding",
+DESCRIPTION = "A package for the management of analyses and data in DNA metabarcoding."
 PYTHONMIN   = '3.5'
 
 SRC       = 'python'
@@ -145,17 +156,24 @@ classifiers=['Development Status :: 4 - Beta',
              'Topic :: Utilities',
              ]
 
+with open("README.md", "r") as fh:
+    long_description = fh.read()
+
 setup(name=PACKAGE,
       description=DESCRIPTION,
+      long_description=long_description,
+      long_description_content_type="text/markdown",
       classifiers=classifiers,
       version=VERSION,
       author=AUTHOR,
       author_email=EMAIL,
+      platforms=PLATFORMS,
       license=LICENSE,
       url=URL,
       ext_modules=xx,
       distclass=Distribution,
       cmdclass={'build': build,
+                'bdist_egg': bdist_egg,
                 'build_clib': build_clib},
       cobitools3=get_python_lib(),
       packages = findPackage('python'),

src/build_reference_db.c

@@ -157,7 +157,7 @@ int build_reference_db(const char* dms_name,
 	ecotx_t* lca_2 = NULL;
 	ecotx_t* lca = NULL;
 	index_t idx1, idx2;
-	index_t i, j, k;
+	index_t i, j, k, count;
 	int32_t taxid_array_length;
 	int32_t score_array_length;
 	int32_t taxid_array_writable_length;
@@ -185,6 +185,7 @@ int build_reference_db(const char* dms_name,
 	matrix_view_name = strcpy(matrix_view_name, o_view_name);
 	strcat(matrix_view_name, "_matrix");
 
+	fprintf(stderr, "Aligning queries with reference database...\n");
 	if (obi_lcs_align_one_column(dms_name,
 								 refs_view_name,
 								 "",
@@ -320,13 +321,19 @@ int build_reference_db(const char* dms_name,
 		return -1;
 	}
 
+	count = (matrix_with_lca_view->infos)->line_count;
+	fprintf(stderr, "Computing LCAs...\n");
+
 	// Compute all the LCAs
 		// For each pair
-	for (i=0; i<(matrix_with_lca_view->infos)->line_count; i++)
+	for (i=0; i<count; i++)
 	{
 		if (! keep_running)
 			return -1;
 
+		if (i%1000 == 0)
+			fprintf(stderr,"\rDone : %f %%       ", (i / (float) count)*100);
+
 		// Read all taxids associated with the first sequence and compute their LCA
 		// Read line index
 		idx1 = obi_get_int_with_elt_idx_and_col_p_in_view(matrix_with_lca_view, matrix_idx1_column, i, 0);
@@ -363,6 +370,7 @@ int build_reference_db(const char* dms_name,
 			return -1;
 		}
 	}
+	fprintf(stderr,"\rDone : 100 %%           \n");
 
 	// Clone refs view, add 2 arrays columns for lca and score, compute and write them
 
@@ -442,13 +450,18 @@ int build_reference_db(const char* dms_name,
 		return -1;
 	}
 
+	fprintf(stderr, "Building LCA arrays...\n");
+
 	// For each sequence, look for all its alignments in the matrix, and for each different LCA taxid/score, order them and write them
 	// Going through matrix once, filling refs arrays on the go for efficiency
-	for (i=0; i<(matrix_with_lca_view->infos)->line_count; i++)
+	for (i=0; i<count; i++)
 	{
 		if (! keep_running)
 			return -1;
 
+		if (i%1000 == 0)
+			fprintf(stderr,"\rDone : %f %%       ", (i / (float) count)*100);
+
 		// Read ref line indexes
 		idx1 = obi_get_int_with_elt_idx_and_col_p_in_view(matrix_with_lca_view, matrix_idx1_column, i, 0);
 		idx2 = obi_get_int_with_elt_idx_and_col_p_in_view(matrix_with_lca_view, matrix_idx2_column, i, 0);
@@ -464,6 +477,8 @@ int build_reference_db(const char* dms_name,
 		// Read alignment score
 		score = obi_get_float_with_elt_idx_and_col_p_in_view(matrix_with_lca_view, matrix_score_column, i, 0);
 
+		//fprintf(stderr, "\n\ntaxid_lca=%d, score=%f, idx1=%d, idx2=%d", taxid_lca, score, idx1, idx2);
+
 		///////////////// Compute for first sequence \\\\\\\\\\\\\\\\\\\\\\\     (TODO function)
 
 		// Read arrays
@@ -480,9 +495,11 @@ int build_reference_db(const char* dms_name,
 //			return -1;
 //		}
 
+		//fprintf(stderr, "\n1st sequence");
 		// If empty, add values
 		if (taxid_array_length == 0)
 		{
+			//fprintf(stderr, "\nEmpty, add value");
 			if (obi_set_array_with_col_p_in_view(o_view, final_lca_taxid_a_column, idx1, &taxid_lca, (uint8_t) (obi_sizeof(OBI_INT) * 8), 1) < 0)
 			{
 				obidebug(1, "\nError setting a LCA taxid array in a column when building a reference database");
@@ -496,6 +513,8 @@ int build_reference_db(const char* dms_name,
 		}
 		else
 		{
+			//fprintf(stderr, "\nNot empty");
+
 			j = 0;
 			modified = false;
 			while (j < taxid_array_length)
@@ -509,6 +528,9 @@ int build_reference_db(const char* dms_name,
 						memcpy(score_array_writable, score_array, score_array_length*sizeof(obifloat_t));
 						modified = true;
 
+						//fprintf(stderr, "\nSame LCA, replace %d and %f with %d and %f", lca_taxid_array_writable[j],
+						//		score_array_writable[j], taxid_lca, score);
+
 						// Better score for the same LCA, replace this LCA/score pair
 						lca_taxid_array_writable[j] = taxid_lca;
 						score_array_writable[j] = score;
@@ -535,6 +557,8 @@ int build_reference_db(const char* dms_name,
 				{
 					if (score > score_array[j])
 					{
+						//fprintf(stderr, "\nInsert new");
+
 						memcpy(lca_taxid_array_writable, lca_taxid_array, taxid_array_length*sizeof(obiint_t));
 						memcpy(score_array_writable, score_array, score_array_length*sizeof(obifloat_t));
 						modified = true;
@@ -579,10 +603,15 @@ int build_reference_db(const char* dms_name,
 				memcpy(score_array_writable, score_array, score_array_length*sizeof(obifloat_t));
 				modified = true;
 
+				//fprintf(stderr, "\nAppend at the end");
+
 				// Append LCA
 				lca_taxid_array_writable[taxid_array_writable_length] = taxid_lca;
 				score_array_writable[score_array_writable_length] = score;
 
+				taxid_array_writable_length++;
+				score_array_writable_length++;
+
 				// Remove the previous (children) LCAs from the array if their score is equal or lower
 				while ((j>0) && (score_array_writable[j-1] <= score))
 				{
@@ -603,6 +632,13 @@ int build_reference_db(const char* dms_name,
 			// Write new arrays
 			if (modified)
 			{
+//				fprintf(stderr, "\n\nnew array:");
+//				for (k=0;k<taxid_array_writable_length;k++)
+//				{
+//					lca = obi_taxo_get_taxon_with_taxid(tax, lca_taxid_array_writable[k]);
+//					fprintf(stderr, "\nLCA=%d, %s, score=%f", lca_taxid_array_writable[k], lca->name, score_array_writable[k]);
+//				}
+
 				if (obi_set_array_with_col_p_in_view(o_view, final_lca_taxid_a_column, idx1, lca_taxid_array_writable, (uint8_t) (obi_sizeof(OBI_INT) * 8), taxid_array_writable_length) < 0)
 				{
 					obidebug(1, "\nError setting a LCA taxid array in a column when building a reference database");
@@ -632,9 +668,13 @@ int build_reference_db(const char* dms_name,
 //			return -1;
 //		}
 
+		//fprintf(stderr, "\n2nd sequence");
+
 		// If empty, add values
 		if (taxid_array_length == 0)
 		{
+			//fprintf(stderr, "\nEmpty, add value");
+
 			if (obi_set_array_with_col_p_in_view(o_view, final_lca_taxid_a_column, idx2, &taxid_lca, (uint8_t) (obi_sizeof(OBI_INT) * 8), 1) < 0)
 			{
 				obidebug(1, "\nError setting a LCA taxid array in a column when building a reference database");
@@ -648,6 +688,8 @@ int build_reference_db(const char* dms_name,
 		}
 		else
 		{
+			//fprintf(stderr, "\nNot empty");
+
 			j = 0;
 			modified = false;
 			while (j < taxid_array_length)
@@ -661,6 +703,9 @@ int build_reference_db(const char* dms_name,
 						memcpy(score_array_writable, score_array, score_array_length*sizeof(obifloat_t));
 						modified = true;
 
+						//fprintf(stderr, "\nSame LCA, replace %d and %f with %d and %f", lca_taxid_array_writable[j],
+						//		score_array_writable[j], taxid_lca, score);
+
 						// Better score for the same LCA, replace this LCA/score pair
 						lca_taxid_array_writable[j] = taxid_lca;
 						score_array_writable[j] = score;
@@ -687,6 +732,8 @@ int build_reference_db(const char* dms_name,
 				{
 					if (score > score_array[j])
 					{
+						//fprintf(stderr, "\nInsert new");
+
 						memcpy(lca_taxid_array_writable, lca_taxid_array, taxid_array_length*sizeof(obiint_t));
 						memcpy(score_array_writable, score_array, score_array_length*sizeof(obifloat_t));
 						modified = true;
@@ -727,6 +774,8 @@ int build_reference_db(const char* dms_name,
 
 			if (j == taxid_array_length) // same or parent LCA not found, need to be appended at the end
 			{
+				//fprintf(stderr, "\nAppend at the end");
+
 				memcpy(lca_taxid_array_writable, lca_taxid_array, taxid_array_length*sizeof(obiint_t));
 				memcpy(score_array_writable, score_array, score_array_length*sizeof(obifloat_t));
 				modified = true;
@@ -735,6 +784,9 @@ int build_reference_db(const char* dms_name,
 				lca_taxid_array_writable[taxid_array_writable_length] = taxid_lca;
 				score_array_writable[score_array_writable_length] = score;
 
+				taxid_array_writable_length++;
+				score_array_writable_length++;
+
 				// Remove the previous (children) LCAs from the array if their score is equal or lower
 				while ((j>0) && (score_array_writable[j-1] <= score))
 				{
@@ -769,11 +821,17 @@ int build_reference_db(const char* dms_name,
 			}
 		}
 	}
+	fprintf(stderr,"\rDone : 100 %%           \n");
 
+	fprintf(stderr, "Writing results...\n");
+	count = (o_view->infos)->line_count;
 	// Fill empty LCA informations (because filling from potentially sparse alignment matrix) with the sequence taxid
 	score=1.0;  // technically getting LCA of identical sequences
-	for (i=0; i<(o_view->infos)->line_count; i++)
+	for (i=0; i<count; i++)
 	{
+		if (i%1000 == 0)
+			fprintf(stderr,"\rDone : %f %%       ", (i / (float) count)*100);
+
 		obi_get_array_with_col_p_in_view(o_view, final_lca_taxid_a_column, i, &taxid_array_length);
 		if (taxid_array_length == 0)  // no LCA set
 		{
@@ -799,6 +857,7 @@ int build_reference_db(const char* dms_name,
 			}
 		}
 	}
+	fprintf(stderr,"\rDone : 100 %%           \n");
 
 	// Add information about the threshold used to build the DB
 	snprintf(threshold_str, 5, "%f", threshold);
@@ -858,7 +917,6 @@ int build_reference_db(const char* dms_name,
 	free(matrix_view_name);
 	free(matrix_with_lca_view_name);
 
-	fprintf(stderr,"\rDone : 100 %%           \n");
 	return 0;
 }
 

src/encode.c

@@ -36,10 +36,12 @@ bool only_ATGC(const char* seq)
 	{
 		if (!((*c == 'A') || \
 			  (*c == 'T') || \
+			  (*c == 'U') || \
 			  (*c == 'G') || \
 			  (*c == 'C') || \
 			  (*c == 'a') || \
 			  (*c == 't') || \
+			  (*c == 'u') || \
 			  (*c == 'g') || \
 			  (*c == 'c')))
 		{
@@ -182,6 +184,8 @@ byte_t* encode_seq_on_2_bits(const char* seq, int32_t length)
 			break;
 		case 't':
 		case 'T':
+		case 'u':
+		case 'U':
 			seq_b[i/4] |= NUC_T_2b;
 			break;
 		default:
@@ -288,6 +292,8 @@ byte_t* encode_seq_on_4_bits(const char* seq, int32_t length)
 			break;
 		case 't':
 		case 'T':
+		case 'u': // discussable
+		case 'U':
 			seq_b[i/2] |= NUC_T_4b;
 			break;
 		case 'r':

src/encode.h

@@ -64,7 +64,7 @@ enum
 
 
 /**
- * @brief Checks if there are only 'atgcATGC' characters in a
+ * @brief Checks if there are only 'atgcuATGCU' characters in a
  *        character string.
  *
  * @param seq The sequence to check.
@@ -129,12 +129,13 @@ byte_t get_nucleotide_from_encoded_seq(byte_t* seq, int32_t idx, uint8_t encodin
 /**
  * @brief Encodes a DNA sequence with each nucleotide coded on 2 bits.
  *
- *    A or a : 00
- *    C or c : 01
- *    T or t : 10
- *    G or g : 11
+ *    A or a :           00
+ *    C or c :           01
+ *    T or t or U or u : 10
+ *    G or g :           11
  *
- * @warning The DNA sequence must contain only 'atgcATGC' characters.
+ * @warning The DNA sequence must contain only 'atgcuATGCU' characters.
+ * @warning Uracil ('U') bases are encoded as Thymine ('T') bases.
  *
  * @param seq The sequence to encode.
  * @param length The length of the sequence to encode.
@@ -169,23 +170,24 @@ char* decode_seq_on_2_bits(byte_t* seq_b, int32_t length_seq);
 /**
  * @brief Encodes a DNA sequence with each nucleotide coded on 4 bits.
  *
- *		A or a : 0001
- *      C or c : 0010
- *      G or g : 0011
- *      T or t : 0100
- *      R or r : 0101
- *      Y or y : 0110
- *      S or s : 0111
- *      W or w : 1000
- *      K or k : 1001
- *      M or m : 1010
- *      B or b : 1011
- *      D or d : 1100
- *      H or h : 1101
- *      V or v : 1110
- *      N or n : 1111
+ *		A or a :           0001
+ *      C or c :           0010
+ *      G or g :           0011
+ *      T or t or U or u : 0100
+ *      R or r :           0101
+ *      Y or y :           0110
+ *      S or s :           0111
+ *      W or w :           1000
+ *      K or k :           1001
+ *      M or m :           1010
+ *      B or b :           1011
+ *      D or d :           1100
+ *      H or h :           1101
+ *      V or v :           1110
+ *      N or n :           1111
  *
  * @warning The DNA sequence must contain only IUPAC characters.
+ * @warning Uracil ('U') bases are encoded as Thymine ('T') bases.
  *
  * @param seq The sequence to encode.
  * @param length The length of the sequence to encode.

src/kmer_similarity.c

@@ -413,7 +413,13 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
 	 	return NULL;
 	}
 
-	score = max_common_kmers + kmer_size - 1;  // aka the number of nucleotides in the longest stretch of kmers perfectly matching
+	if (max_common_kmers > 0)
+		score = max_common_kmers + kmer_size - 1; // aka an approximation of the number of nucleotides matching in the overlap of the alignment.
+												  // It's an approximation because one mismatch produces kmer_size kmer mismatches if in the middle of the overlap,
+												  // and less for mismatches located towards the ends of the overlap. The case where there are the most mismatches is assumed,
+												  // meaning that the score will be often underestimated and never overestimated.
+	else
+		score = 0;
 	abs_shift = abs(best_shift);
 
 	// Save result in Obi_ali structure
@@ -423,10 +429,15 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
 	ali->shift = abs_shift;
 	ali->consensus_seq = NULL;
 	ali->consensus_qual = NULL;
-	if (((best_shift <= 0) && (!switched_seqs)) || ((best_shift > 0) && switched_seqs))
-		strcpy(ali->direction, "left");
+	if (score == 0)
+		ali->direction[0] = '\0';
 	else
-		strcpy(ali->direction, "right");
+	{
+		if (((best_shift <= 0) && (!switched_seqs)) || ((best_shift > 0) && switched_seqs))
+			strcpy(ali->direction, "left");
+		else
+			strcpy(ali->direction, "right");
+	}
 
 	// Build the consensus sequence if asked
 	if (build_consensus)

src/kmer_similarity.h

@@ -27,7 +27,11 @@
  * @brief Alignment structure, with informations about the similarity and to rebuild the alignment.
  */
 typedef struct Obi_ali {
-	int      score;	    		/**< Alignment score, corresponding to the number of nucleotides in the longest stretch of kmers perfectly matching.
+	int      score;	    		/**< Alignment score, corresponding to an approximation of the number of
+								 *   nucleotides matching in the overlap of the alignment.
+								 *   It's an approximation because one mismatch produces kmer_size kmer mismatches if in the middle of the overlap,
+							     *   and less for mismatches located towards the ends of the overlap. The case where there are the most mismatches is assumed,
+							     *   meaning that the score will be often underestimated and never overestimated.
 	 	 	 	 	 	 	 	 */
 	int      consensus_length; 	/**< Length of the final consensus sequence.
 	 	 	 	 	 	 	 	 */

src/obi_clean.c

@@ -246,7 +246,16 @@ int obi_clean(const char* dms_name,
 
 	// Open the sample column if there is one
 	if ((strcmp(sample_column_name, "") == 0) || (sample_column_name == NULL))
-		sample_column = NULL;
+	{
+		fprintf(stderr, "Info: No sample information provided, assuming one sample.\n");
+		sample_column = obi_view_get_column(i_view, COUNT_COLUMN);
+		if (sample_column == NULL)
+		{
+			obidebug(1, "\nError getting the COUNT column");
+			return -1;
+		}
+		sample_count = 1;
+	}
 	else
 	{
 		sample_column = obi_view_get_column(i_view, sample_column_name);
@@ -255,6 +264,13 @@ int obi_clean(const char* dms_name,
 			obidebug(1, "\nError getting the sample column");
 			return -1;
 		}
+		sample_count = (sample_column->header)->nb_elements_per_line;
+		// Check that the sample column is a merged column with all sample informations
+		if (sample_count == 1)
+		{
+			obidebug(1, "\n\nError: If a sample column is provided, it must contain 'merged' sample counts as built by obi uniq with the -m option\n");
+			return -1;
+		}
 	}
 
 	// Create the output view, or a temporary one if heads only
@@ -279,8 +295,6 @@ int obi_clean(const char* dms_name,
 		return -1;
 	}
 
-	sample_count = (sample_column->header)->nb_elements_per_line;
-
 	// Create the output columns
 	if (create_output_columns(o_view, sample_column, sample_count) < 0)
 	{
@@ -409,8 +423,7 @@ int obi_clean(const char* dms_name,
 			stop = true;
 		}
 
-		#pragma omp parallel default(none) \
-					 	 	 shared(thread_count, seq_count, blob_array, complete_sample_count_array, alignment_result_array, \
+		#pragma omp parallel shared(thread_count, seq_count, blob_array, complete_sample_count_array, alignment_result_array, \
 					 	 			 stop, blob1, i, obi_errno, keep_running, stderr, max_ratio, iseq_column, i_view, \
 									 similarity_mode, reference, normalize, threshold, ktable, status_column, o_view, sample_count)
 		{
@@ -550,7 +563,7 @@ int obi_clean(const char* dms_name,
 
 	if (heads_only)
 	{
-		line_selection = malloc((o_view->infos)->line_count * sizeof(index_t));
+		line_selection = malloc((((o_view->infos)->line_count) + 1) * sizeof(index_t));
 		if (line_selection == NULL)
 		{
 			obi_set_errno(OBI_MALLOC_ERROR);

src/obi_clean.h

@@ -52,7 +52,8 @@
  *
  * @param dms A pointer on an OBIDMS.
  * @param i_view_name The name of the input view.
- * @param sample_column_name The name of the OBI_STR column in the input view where the sample information is kept.
+ * @param sample_column_name The name of the column in the input view where the sample information is kept.
+ *                           Must be merged informations as built by the obi uniq tool (checked by the function).
  *                           NULL or "" (empty string) if there is no sample information.
  * @param o_view_name The name of the output view where the results should be written (should not already exist).
  * @param o_view_comments The comments that should be associated with the output view.

src/obi_ecopcr.c

@@ -77,7 +77,8 @@ static int create_output_columns(Obiview_p o_view, bool kingdom_mode);
  * @param err2 The number of errors in the second primer.
  * @param strand The DNA strand direction of the amplicon (R(everse) or D(irect)).
  * @param kingdom_mode Whether the kingdom or the superkingdom informations should be printed to the output.
- * @param keep_nucleotides Number of nucleotides kept on each side of the amplicon.
+ * @param keep_nucleotides Number of nucleotides kept on each side of the amplicon (not including the primers if they are kept).
+ * @param keep_primers Whether to keep the primers.
  * @param i_id_column A pointer on the input sequence identifier column.
  * @param o_id_column A pointer on the output sequence identifier column.
  * @param o_ori_seq_len_column A pointer on the original sequence length column.
@@ -104,7 +105,8 @@ static int create_output_columns(Obiview_p o_view, bool kingdom_mode);
  * @param o_temp1_column A pointer on the output column for the temperature for the first primer.
  * @param o_temp2_column A pointer on the output column for the temperature for the second primer.
  *
- * @retval 0 if the operation was successfully completed.
+ * @retval 0 if the sequence was skipped (taxid not found, warning printed).
+ * @retval 1 if the sequence was successfully printed to the output.
  * @retval -1 if an error occurred.
  *
  * @since July 2018
@@ -124,6 +126,7 @@ static int print_seq(Obiview_p i_view, Obiview_p o_view,
 					 int32_t err1, int32_t err2,
 					 char strand, bool kingdom_mode,
 					 int keep_nucleotides,
+					 bool keep_primers,
 					 OBIDMS_column_p i_id_column, OBIDMS_column_p o_id_column, OBIDMS_column_p o_ori_seq_len_column,
 					 OBIDMS_column_p o_amplicon_column, OBIDMS_column_p o_amplicon_length_column,
 					 OBIDMS_column_p o_taxid_column, OBIDMS_column_p o_rank_column, OBIDMS_column_p o_name_column,
@@ -328,6 +331,7 @@ static int print_seq(Obiview_p i_view, Obiview_p o_view,
 					 int32_t err1, int32_t err2,
 					 char strand, bool kingdom_mode,
 					 int keep_nucleotides,
+					 bool keep_primers,
 					 OBIDMS_column_p i_id_column, OBIDMS_column_p o_id_column, OBIDMS_column_p o_ori_seq_len_column,
 					 OBIDMS_column_p o_amplicon_column, OBIDMS_column_p o_amplicon_length_column,
 					 OBIDMS_column_p o_taxid_column, OBIDMS_column_p o_rank_column, OBIDMS_column_p o_name_column,
@@ -363,6 +367,17 @@ static int print_seq(Obiview_p i_view, Obiview_p o_view,
 
 	// TODO add check for primer longer than MAX_PAT_LEN (32)
 
+	// Get sequence id
+	seq_id = obi_get_str_with_elt_idx_and_col_p_in_view(i_view, i_id_column, i_idx, 0);
+
+	// Get the taxon structure
+	main_taxon = obi_taxo_get_taxon_with_taxid(taxonomy, taxid);
+	if (main_taxon == NULL)
+	{
+		obidebug(1, "\nWarning: error reading the taxonomic information of a sequence. Seq id: %s, taxid: %d. Probably deprecated taxid. Skipping this sequence.", seq_id, taxid);
+		return 0;
+	}
+
 	ldelta = (pos1 <= keep_nucleotides)?pos1:keep_nucleotides;
 	rdelta = ((pos2+keep_nucleotides)>=seq_len)?seq_len-pos2:keep_nucleotides;
 
@@ -382,7 +397,7 @@ static int print_seq(Obiview_p i_view, Obiview_p o_view,
 		oligo2[o1->patlen] = 0;
 		error2 = err1;
 
-		if (keep_nucleotides == 0)
+		if (!keep_primers)
 			amplicon+=o2->patlen;
 		else
 		{
@@ -401,7 +416,7 @@ static int print_seq(Obiview_p i_view, Obiview_p o_view,
 		oligo2[o2->patlen] = 0;
 		error2 = err2;
 
-		if (keep_nucleotides==0)
+		if (!keep_primers)
 			amplicon+=o1->patlen;
 		else
 		{
@@ -411,16 +426,11 @@ static int print_seq(Obiview_p i_view, Obiview_p o_view,
 	}
 
 	ecoComplementSequence(oligo2);
-	if (keep_nucleotides == 0)
+	if (!keep_primers)
 		amplicon[amplicon_len]=0;
 	else
 	{
 		amplicon_len = ldelta+rdelta+amplicon_len;
-		for (i=0; i<ldelta; i++)
-			amplicon[i]|=32;
-		for (i=1; i<=rdelta; i++)
-			amplicon[amplicon_len-i]|=32;
-
 		amplicon[amplicon_len] = 0;
 	}
 
@@ -433,16 +443,7 @@ static int print_seq(Obiview_p i_view, Obiview_p o_view,
 	if (isnan(tm2))
 		tm2 = OBIFloat_NA;
 
-	// Get the taxon structure
-	main_taxon = obi_taxo_get_taxon_with_taxid(taxonomy, taxid);
-	if (main_taxon == NULL)
-	{
-		obidebug(1, "\nError reading the taxonomic information of a sequence");
-		return -1;
-	}
-
 	// Write sequence id
-	seq_id = obi_get_str_with_elt_idx_and_col_p_in_view(i_view, i_id_column, i_idx, 0);
 	if (obi_set_str_with_elt_idx_and_col_p_in_view(o_view, o_id_column, o_idx, 0, seq_id) < 0)
 	{
 		obidebug(1, "\nError writing the sequence id");
@@ -631,7 +632,7 @@ static int print_seq(Obiview_p i_view, Obiview_p o_view,
 		return -1;
 	}
 
-	return 0;
+	return 1;
 }
 
 
@@ -659,6 +660,7 @@ int obi_ecopcr(const char* i_dms_name,
 			   double salt,
 			   int saltmethod,
 			   int keep_nucleotides,
+			   bool keep_primers,
 			   bool kingdom_mode)
 {
 
@@ -699,6 +701,7 @@ int obi_ecopcr(const char* i_dms_name,
 
 	obiint_t      taxid;
 	char*         sequence;
+	int			  printed;
 
 	SeqPtr        apatseq=NULL;
 	int32_t       o1Hits;
@@ -717,6 +720,9 @@ int obi_ecopcr(const char* i_dms_name,
 
 	signal(SIGINT, sig_handler);
 
+	if (keep_nucleotides > 0)
+		keep_primers = true;
+
 	if (circular)
 	{
 		circular = strlen(primer1);
@@ -1055,14 +1061,14 @@ int obi_ecopcr(const char* i_dms_name,
 											length = 0;
 											if (posj > posi)
 												length = posj - posi - o1->patlen - o2->patlen;
-											if (posj < posi)
+											else if (circular > 0)
 												length = posj + apatseq->seqlen - posi - o1->patlen - o2->patlen;
 											if ((length>0) &&	// For when primers touch or overlap
 												(!min_len || (length >= min_len)) &&
 												(!max_len || (length <= max_len)))
 											{
 												// Print the found amplicon
-												if (print_seq(i_view, o_view,
+												printed = print_seq(i_view, o_view,
 														  	  i_idx, o_idx,
 															  taxonomy,
 															  sequence,
@@ -1076,6 +1082,7 @@ int obi_ecopcr(const char* i_dms_name,
 														  	  erri, errj,
 															  'D', kingdom_mode,
 															  keep_nucleotides,
+															  keep_primers,
 															  i_id_column, o_id_column, o_ori_seq_len_column,
 															  o_amplicon_column, o_amplicon_length_column,
 															  o_taxid_column, o_rank_column, o_name_column,
@@ -1087,12 +1094,14 @@ int obi_ecopcr(const char* i_dms_name,
 															  o_strand_column,
 															  o_primer1_column, o_primer2_column,
 															  o_error1_column, o_error2_column,
-															  o_temp1_column,  o_temp2_column) < 0)
+															  o_temp1_column,  o_temp2_column);
+												if (printed < 0)
 												{
 													obidebug(1, "\nError writing the ecopcr result");
 													return -1;
 												}
-												o_idx++;
+												else if (printed > 0)
+													o_idx++;
 											}
 										}
 									}
@@ -1142,14 +1151,14 @@ int obi_ecopcr(const char* i_dms_name,
 											length = 0;
 											if (posj > posi)
 												length = posj - posi + 1  - o2->patlen - o1->patlen; /* - o1->patlen : deleted by <EC> (prior to the OBITools3) */
-											if (posj < posi)
+											else if (circular > 0)
 												length = posj + apatseq->seqlen - posi - o1->patlen - o2->patlen;
 											if ((length>0) &&	// For when primers touch or overlap
 												(!min_len || (length >= min_len)) &&
 												(!max_len || (length <= max_len)))
 											{
 												// Print the found amplicon
-												if (print_seq(i_view, o_view,
+												printed = print_seq(i_view, o_view,
 														  	  i_idx, o_idx,
 															  taxonomy,
 															  sequence,
@@ -1163,6 +1172,7 @@ int obi_ecopcr(const char* i_dms_name,
 														  	  erri, errj,
 															  'R', kingdom_mode,
 															  keep_nucleotides,
+															  keep_primers,
 															  i_id_column, o_id_column, o_ori_seq_len_column,
 															  o_amplicon_column, o_amplicon_length_column,
 															  o_taxid_column, o_rank_column, o_name_column,
@@ -1174,12 +1184,14 @@ int obi_ecopcr(const char* i_dms_name,
 															  o_strand_column,
 															  o_primer1_column, o_primer2_column,
 															  o_error1_column, o_error2_column,
-															  o_temp1_column,  o_temp2_column) < 0)
+															  o_temp1_column,  o_temp2_column);
+												if (printed < 0)
 												{
 													obidebug(1, "\nError writing the ecopcr result");
 													return -1;
 												}
-												o_idx++;
+												else if (printed > 0)
+													o_idx++;
 											}
 										}
 									}
@@ -1220,7 +1232,7 @@ int obi_ecopcr(const char* i_dms_name,
 		return -1;
 	}
 
-	fprintf(stderr,"\rDone : 100 %%           ");
+	fprintf(stderr,"\rDone : 100 %%           \n");
 	return 0;
 
 	return 0;

src/obi_ecopcr.h

@@ -81,8 +81,8 @@
  * @param o_dms_name The path to the output DMS.
  * @param o_view_name The name of the output view.
  * @param o_view_comments The comments to associate with the output view.
- * @param primer1 The first primer.
- * @param primer2 The second primer.
+ * @param primer1 The first primer, length must be less than or equal to 32 (because of apat lib limitation).
+ * @param primer2 The second primer, length must be less than or equal to 32 (because of apat lib limitation).
  * @param error_max The maximum number of errors allowed per primer for amplification.
  * @param min_len The minimum length of an amplicon.
  * @param max_len The maximum length of an amplicon.
@@ -93,8 +93,8 @@
  * @param salt_concentration The salt concentration used for estimating the Tm.
  * @param salt_correction_method The method used for estimating the Tm (melting temperature) between the primers and their corresponding
  *                              target sequences. SANTALUCIA: 1, or OWCZARZY: 2.
- * @param keep_nucleotides The number of nucleotides to keep on each side of the in silico amplified sequences
- *                         (already including the amplified DNA fragment plus the two target sequences of the primers).
+ * @param keep_nucleotides The number of nucleotides to keep on each side of the in silico amplified sequences, not including primers (primers automatically entirely kept if > 0).
+ * @param keep_primers Whether primers are kept attached to the output sequences.
  * @param kingdom_mode Whether the kingdom or the superkingdom informations should be printed to the output.
  *
  * @returns A value indicating the success of the operation.
@@ -121,6 +121,7 @@ int obi_ecopcr(const char* i_dms_name,
 			   double salt_concentration,
 			   int salt_correction_method,
 			   int keep_nucleotides,
+			   bool keep_primers,
 			   bool kingdom_mode);
 
 #endif /* OBI_ECOPCR_H_ */

src/obi_ecotag.c

@@ -71,9 +71,12 @@ static int create_output_columns(Obiview_p o_view);
  * @param name The assigned scientific name.
  * @param assigned_status_column A pointer on the column where the assigned status should be written.
  * @param assigned The assigned status (whether the sequence was assigned to a taxon or not).
- * @param best_match_column A pointer on the column where the list of ids of the best matches should be written.
+ * @param best_match_ids_column A pointer on the column where the list of ids of the best matches should be written.
  * @param best_match_ids The list of ids of the best matches as an array of the concatenated ids separated by '\0'.
  * @param best_match_ids_length The total length of the array of ids of best matches.
+ * @param best_match_taxids_column A pointer on the column where the list of taxids of the best matches should be written.
+ * @param best_match_taxids The list of taxids of the best matches as an array of the taxids.
+ * @param best_match_taxids_length The length of the array of taxids of best matches.
  * @param score_column A pointer on the column where the score should be written.
  * @param score The similarity score of the sequence with its best match(es).
  *
@@ -87,7 +90,8 @@ int print_assignment_result(Obiview_p output_view, index_t line,
 							OBIDMS_column_p assigned_taxid_column, int32_t taxid,
 							OBIDMS_column_p assigned_name_column, const char* name,
 							OBIDMS_column_p assigned_status_column, bool assigned,
-							OBIDMS_column_p best_match_column, const char* best_match_ids, int best_match_ids_length,
+							OBIDMS_column_p best_match_ids_column, const char* best_match_ids, int best_match_ids_length,
+							OBIDMS_column_p best_match_taxids_column, const int32_t* best_match_taxids, int best_match_taxids_length,
 							OBIDMS_column_p score_column, double score);
 
 
@@ -100,37 +104,44 @@ int print_assignment_result(Obiview_p output_view, index_t line,
 static int create_output_columns(Obiview_p o_view)
 {
 	// Score column
-	if (obi_view_add_column(o_view, ECOTAG_SCORE_COLUMN_NAME, -1, NULL, OBI_FLOAT, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOTAG_SCORE_COLUMN_NAME, true) < 0)
+	if (obi_view_add_column(o_view, ECOTAG_SCORE_COLUMN_NAME, -1, NULL, OBI_FLOAT, 0, 1, NULL, false, false, false, NULL, NULL, -1, "{}", true) < 0)
 	{
 		obidebug(1, "\nError creating the column for the score in ecotag");
 		return -1;
 	}
 
 	// Assigned taxid column
-	if (obi_view_add_column(o_view, ECOTAG_TAXID_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOTAG_TAXID_COLUMN_NAME, true) < 0)
+	if (obi_view_add_column(o_view, ECOTAG_TAXID_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, "{}", true) < 0)
 	{
 		obidebug(1, "\nError creating the column for the assigned taxid in ecotag");
 		return -1;
 	}
 
 	// Assigned scientific name column
-	if (obi_view_add_column(o_view, ECOTAG_NAME_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOTAG_NAME_COLUMN_NAME, true) < 0)
+	if (obi_view_add_column(o_view, ECOTAG_NAME_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, NULL, NULL, -1, "{}", true) < 0)
 	{
 		obidebug(1, "\nError creating the column for the assigned scientific name in ecotag");
 		return -1;
 	}
 
 	// Assignement status column
-	if (obi_view_add_column(o_view, ECOTAG_STATUS_COLUMN_NAME, -1, NULL, OBI_BOOL, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOTAG_STATUS_COLUMN_NAME, true) < 0)
+	if (obi_view_add_column(o_view, ECOTAG_STATUS_COLUMN_NAME, -1, NULL, OBI_BOOL, 0, 1, NULL, false, false, false, NULL, NULL, -1, "{}", true) < 0)
 	{
 		obidebug(1, "\nError creating the column for the assignment status in ecotag");
 		return -1;
 	}
 
 	// Column for array of best match ids
-	if (obi_view_add_column(o_view, ECOTAG_BEST_MATCH_IDS_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, true, false, NULL, NULL, -1, ECOTAG_BEST_MATCH_IDS_COLUMN_NAME, true) < 0)
+	if (obi_view_add_column(o_view, ECOTAG_BEST_MATCH_IDS_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, true, false, NULL, NULL, -1, "{}", true) < 0)
 	{
-		obidebug(1, "\nError creating the column for the array of ids of the best match in ecotag");
+		obidebug(1, "\nError creating the column for the array of ids of best matches in ecotag");
+		return -1;
+	}
+
+	// Column for array of best match taxids
+	if (obi_view_add_column(o_view, ECOTAG_BEST_MATCH_TAXIDS_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, true, false, NULL, NULL, -1, "{}", true) < 0)
+	{
+		obidebug(1, "\nError creating the column for the array of taxids of best matches in ecotag");
 		return -1;
 	}
 
@@ -142,7 +153,8 @@ int print_assignment_result(Obiview_p output_view, index_t line,
 							OBIDMS_column_p assigned_taxid_column, int32_t taxid,
 							OBIDMS_column_p assigned_name_column, const char* name,
 							OBIDMS_column_p assigned_status_column, bool assigned,
-							OBIDMS_column_p best_match_column, const char* best_match_ids, int best_match_ids_length,
+							OBIDMS_column_p best_match_ids_column, const char* best_match_ids, int best_match_ids_length,
+							OBIDMS_column_p best_match_taxids_column, const int32_t* best_match_taxids, int best_match_taxids_length,
 							OBIDMS_column_p score_column, double score)
 {
 	// Write the assigned taxid
@@ -167,9 +179,16 @@ int print_assignment_result(Obiview_p output_view, index_t line,
 	}
 
 	// Write the best match ids
-	if (obi_set_array_with_col_p_in_view(output_view, best_match_column, line, best_match_ids, (uint8_t)(sizeof(char)*8), best_match_ids_length) < 0)
+	if (obi_set_array_with_col_p_in_view(output_view, best_match_ids_column, line, best_match_ids, (uint8_t)(sizeof(char)*8), best_match_ids_length) < 0)
 	{
-		obidebug(1, "\nError writing a assignment status in a column when writing ecotag results");
+		obidebug(1, "\nError writing the array of best match ids in a column when writing ecotag results");
+		return -1;
+	}
+
+	// Write the best match taxids
+	if (obi_set_array_with_col_p_in_view(output_view, best_match_taxids_column, line, best_match_taxids, (uint8_t)(sizeof(OBI_INT)*8), best_match_taxids_length) < 0)
+	{
+		obidebug(1, "\nError writing the array of best match taxids in a column when writing ecotag results");
 		return -1;
 	}
 
@@ -199,7 +218,8 @@ int obi_ecotag(const char* dms_name,
 			   const char* taxonomy_name,
 			   const char* output_view_name,
 			   const char* output_view_comments,
-			   double ecotag_threshold)    // TODO different threshold for the similarity sphere around ref seqs
+			   double ecotag_threshold,
+			   double bubble_threshold)
 {
 
 	// For each sequence
@@ -220,6 +240,7 @@ int obi_ecotag(const char* dms_name,
 	index_t         query_seq_idx, ref_seq_idx;
 	double          score, best_score;
 	double			threshold;
+	double			lca_threshold;
 	int             lcs_length;
 	int             ali_length;
 	Kmer_table_p    ktable;
@@ -235,6 +256,8 @@ int obi_ecotag(const char* dms_name,
 	char*     		best_match_ids;
 	char*			best_match_ids_to_store;
 	int32_t         best_match_ids_length;
+	int32_t*   		best_match_taxids;
+	int32_t*		best_match_taxids_to_store;
 	int				best_match_count;
 	int             buffer_size;
 	int 			best_match_ids_buffer_size;
@@ -263,7 +286,8 @@ int obi_ecotag(const char* dms_name,
 	OBIDMS_column_p assigned_taxid_column = NULL;
 	OBIDMS_column_p assigned_name_column = NULL;
 	OBIDMS_column_p assigned_status_column = NULL;
-	OBIDMS_column_p best_match_column = NULL;
+	OBIDMS_column_p best_match_ids_column = NULL;
+	OBIDMS_column_p best_match_taxids_column = NULL;
 	OBIDMS_column_p lca_taxid_a_column = NULL;
 	OBIDMS_column_p score_a_column = NULL;
 	OBIDMS_column_p ref_taxid_column = NULL;
@@ -367,10 +391,10 @@ int obi_ecotag(const char* dms_name,
 		return -1;
 	}
 	free(db_threshold_str);
-	if (ecotag_threshold < db_threshold)
+	if (bubble_threshold < db_threshold)
 	{
 		fprintf(stderr, "\nError: The threshold demanded (%f) is lower than the threshold used to build the reference database (%f).\n\n",
-				ecotag_threshold, db_threshold);
+				bubble_threshold, db_threshold);
 		return -1;
 	}
 
@@ -396,7 +420,8 @@ int obi_ecotag(const char* dms_name,
 	assigned_taxid_column = obi_view_get_column(output_view, ECOTAG_TAXID_COLUMN_NAME);
 	assigned_name_column = obi_view_get_column(output_view, ECOTAG_NAME_COLUMN_NAME);
 	assigned_status_column = obi_view_get_column(output_view, ECOTAG_STATUS_COLUMN_NAME);
-	best_match_column = obi_view_get_column(output_view, ECOTAG_BEST_MATCH_IDS_COLUMN_NAME);
+	best_match_ids_column = obi_view_get_column(output_view, ECOTAG_BEST_MATCH_IDS_COLUMN_NAME);
+	best_match_taxids_column = obi_view_get_column(output_view, ECOTAG_BEST_MATCH_TAXIDS_COLUMN_NAME);
 	score_column = obi_view_get_column(output_view, ECOTAG_SCORE_COLUMN_NAME);
 
 	// Open the used reference columns
@@ -453,9 +478,17 @@ int obi_ecotag(const char* dms_name,
 		return -1;
 	}
 
+	best_match_taxids = (int32_t*) malloc(buffer_size* sizeof(int32_t));
+	if (best_match_taxids == NULL)
+	{
+		obi_set_errno(OBI_MALLOC_ERROR);
+		obidebug(1, "\nError allocating memory for the best match taxid array in ecotag");
+		return -1;
+	}
+
 	for (i=0; i < query_count; i++)
 	{
-		if (i%100 == 0)
+		if (i%1000 == 0)
 			fprintf(stderr,"\rDone : %f %%       ", (i / (float) query_count)*100);
 
 		best_match_count = 0;
@@ -514,7 +547,7 @@ int obi_ecotag(const char* dms_name,
 
 				// Store in best match array
 
-				// Grow match array if needed
+				// Grow match and taxid array if needed
 				if (best_match_count == buffer_size)
 				{
 					buffer_size = buffer_size*2;
@@ -525,6 +558,13 @@ int obi_ecotag(const char* dms_name,
 						obidebug(1, "\nError reallocating match array when assigning");
 						return -1;
 					}
+					best_match_taxids = (int32_t*) realloc(best_match_taxids, buffer_size*sizeof(int32_t));
+					if (best_match_taxids == NULL)
+					{
+						obi_set_errno(OBI_MALLOC_ERROR);
+						obidebug(1, "\nError reallocating match taxids array when assigning");
+						return -1;
+					}
 				}
 
 				id = obi_get_str_with_elt_idx_and_col_p_in_view(ref_view, ref_id_column, j, 0);
@@ -545,6 +585,7 @@ int obi_ecotag(const char* dms_name,
 
 				// Save match
 				best_match_array[best_match_count] = j;
+				best_match_taxids[best_match_count] = obi_get_int_with_elt_idx_and_col_p_in_view(ref_view, ref_taxid_column, j, 0);
 				best_match_count++;
 				strcpy(best_match_ids+best_match_ids_length, id);
 				best_match_ids_length = best_match_ids_length + id_len + 1;
@@ -558,11 +599,16 @@ int obi_ecotag(const char* dms_name,
 		{
 			best_match_idx = best_match_array[j];
 
-			// Find the LCA for the chosen threshold
+			// Find the LCA for the highest threshold between best_score and the chosen bubble threshold
 			score_array = obi_get_array_with_col_p_in_view(ref_view, score_a_column, best_match_idx, &lca_array_length);
 
+			if (bubble_threshold < best_score)
+				lca_threshold = best_score;
+			else
+				lca_threshold = bubble_threshold;
+
 			k = 0;
-			while ((k < lca_array_length) && (score_array[k] >= ecotag_threshold))
+			while ((k < lca_array_length) && (score_array[k] >= lca_threshold))
 				k++;
 
 			if (k>0)
@@ -570,12 +616,12 @@ int obi_ecotag(const char* dms_name,
 				lca_array = obi_get_array_with_col_p_in_view(ref_view, lca_taxid_a_column, best_match_idx, &lca_array_length);
 				if (j>0)
 				{
-					lca = obi_taxo_get_taxon_with_taxid(taxonomy, lca_taxid);
-					if (lca == NULL)
-					{
-						obidebug(1, "\nError getting a taxon from a taxid when doing taxonomic assignment");
-						return -1;
-					}
+//					lca = obi_taxo_get_taxon_with_taxid(taxonomy, lca_taxid);
+//					if (lca == NULL)
+//					{
+//						obidebug(1, "\nError getting a taxon from a taxid when doing taxonomic assignment");
+//						return -1;
+//					}
 					lca_in_array = obi_taxo_get_taxon_with_taxid(taxonomy, lca_array[k-1]);
 					if (lca_in_array == NULL)
 					{
@@ -629,6 +675,7 @@ int obi_ecotag(const char* dms_name,
 			else
 				lca_name = lca->name;
 			best_match_ids_to_store = best_match_ids;
+			best_match_taxids_to_store = best_match_taxids;
 		}
 		else
 		{
@@ -636,6 +683,7 @@ int obi_ecotag(const char* dms_name,
 			lca_name = OBIStr_NA;
 			lca_taxid = OBIInt_NA;
 			best_match_ids_to_store = OBITuple_NA;
+			best_match_taxids_to_store = OBITuple_NA;
 			score = OBIFloat_NA;
 		}
 
@@ -644,7 +692,8 @@ int obi_ecotag(const char* dms_name,
 								    assigned_taxid_column, lca_taxid,
 									assigned_name_column, lca_name,
 									assigned_status_column, assigned,
-									best_match_column, best_match_ids_to_store, best_match_ids_length,
+									best_match_ids_column, best_match_ids_to_store, best_match_ids_length,
+									best_match_taxids_column, best_match_taxids_to_store, best_match_count,
 									score_column, best_score
 									) < 0)
 							return -1;
@@ -652,6 +701,7 @@ int obi_ecotag(const char* dms_name,
 
 	free(best_match_array);
 	free(best_match_ids);
+	free(best_match_taxids);
 
 	obi_close_taxonomy(taxonomy);
 	obi_save_and_close_view(query_view);

src/obi_ecotag.h

@@ -23,7 +23,8 @@
 #define ECOTAG_TAXID_COLUMN_NAME "TAXID"
 #define ECOTAG_NAME_COLUMN_NAME "SCIENTIFIC_NAME"
 #define ECOTAG_STATUS_COLUMN_NAME "ID_STATUS"
-#define ECOTAG_BEST_MATCH_IDS_COLUMN_NAME "BEST_MATCH"
+#define ECOTAG_BEST_MATCH_IDS_COLUMN_NAME "BEST_MATCH_IDS"
+#define ECOTAG_BEST_MATCH_TAXIDS_COLUMN_NAME "BEST_MATCH_TAXIDS"
 #define ECOTAG_SCORE_COLUMN_NAME "BEST_IDENTITY"
 
 
@@ -41,12 +42,14 @@
  * @param output_view_name The name to give to the output view.
  * @param output_view_comments The comments to associate to the output view.
  * @param ecotag_threshold The threshold at which to assign.
+ * @param bubble_threshold The threshold at which to look for an LCA (i.e. minimum identity considered for the assignment circle);
+ *                         the threshold actually used will be the highest between this value and the best assignment score found.
  *
  * 	The algorithm works like this:
  * 		For each query sequence:
  *			Align with reference database
  *			Keep the indices of all the best matches
- *			For each kept index, get the LCA at that threshold as stored in the reference database, then the LCA of those LCAs
+ *			For each kept index, get the LCA at the highest threshold between bubble_threshold and the best assignment score found (as stored in the reference database), then the LCA of those LCAs
  *			Write result (max score, threshold, taxid and scientific name of the LCA assigned, list of the ids of the best matches)
  *
  * @returns A value indicating the success of the operation.
@@ -64,7 +67,8 @@ int obi_ecotag(const char* dms_name,
 			   const char* taxonomy_name,
 			   const char* output_view_name,
 			   const char* output_view_comments,
-			   double ecotag_threshold);
+			   double ecotag_threshold,
+			   double bubble_threshold);
 
 
 #endif /* OBI_ECOTAG_H_ */

src/obiavl.c

@@ -648,7 +648,7 @@ int truncate_avl_data_to_size_used(OBIDMS_avl_data_p avl_data)	// TODO is it nec
 	new_data_size = ((index_t) multiple) * getpagesize();
 
 	// Check that it is actually greater than the current size of the file, otherwise no need to truncate
-	if ((avl_data->header)->data_size_max == new_data_size)
+	if ((avl_data->header)->data_size_max >= new_data_size)
 		return 0;
 
 	// Get the file descriptor
@@ -667,7 +667,7 @@ int truncate_avl_data_to_size_used(OBIDMS_avl_data_p avl_data)	// TODO is it nec
 	if (ftruncate(file_descriptor, file_size) < 0)
 	{
 		obi_set_errno(OBI_AVL_ERROR);
-		obidebug(1, "\nError truncating an AVL data file");
+		obidebug(1, "\nError truncating an AVL data file, old data size = %lld, new data size = %lld", (avl_data->header)->data_size_max, new_data_size);
 		return -1;
 	}
 
@@ -2259,7 +2259,13 @@ index_t obi_avl_add(OBIDMS_avl_p avl, Obi_blob_p value)
 		parent = next;
 
 		// Compare the crc of the value with the crc of the current node
-		comp = (current_node->crc64) - crc;
+		//comp = (current_node->crc64) - crc;
+		if ((current_node->crc64) == crc)
+			comp = 0;
+		else if ((current_node->crc64) > crc)
+			comp = 1;
+		else
+			comp = -1;
 
 		if (comp == 0)
 		{ // check if really same value
@@ -2354,7 +2360,13 @@ index_t obi_avl_find(OBIDMS_avl_p avl, Obi_blob_p value)
 		current_node = (avl->tree)+next;
 
 		// Compare the crc of the value with the crc of the current node
-		comp = (current_node->crc64) - crc;
+		//comp = (current_node->crc64) - crc;
+		if ((current_node->crc64) == crc)
+			comp = 0;
+		else if ((current_node->crc64) > crc)
+			comp = 1;
+		else
+			comp = -1;
 
 		if (comp == 0)
 		{ // Check if really same value

src/obidms.c

@@ -696,6 +696,12 @@ int obi_clean_dms(const char* dms_path)
 //		return -1;
 //	}
 
+	if (obi_close_dms(dms, true) < 0)
+	{
+		obidebug(1, "\nError closing a DMS after cleaning");
+		return -1;
+	}
+
 	return 0;
 }
 
@@ -1403,6 +1409,107 @@ DIR* opendir_in_dms(OBIDMS_p dms, const char* path_name)
 }
 
 
+char* obi_dms_formatted_infos(OBIDMS_p dms, bool detailed)
+{
+	char*          dms_infos = NULL;
+	char*   	   view_infos = NULL;
+	char*          view_name = NULL;
+	char*          tax_name = NULL;
+	char*          all_tax_dir_path = NULL;
+	int            i;
+	struct dirent* dp;
+	Obiview_p      view;
+
+	// DMS name
+	dms_infos = (char*) malloc((strlen("# DMS name: ")+strlen(dms->dms_name)+strlen("\n# Views:\n")+1) * sizeof(char));
+	if (dms_infos == NULL)
+	{
+		obidebug(1, "\nError allocating memory for DMS formatted infos");
+		return NULL;
+	}
+	strcpy(dms_infos, "# DMS name: ");
+	strcat(dms_infos, dms->dms_name);
+	strcat(dms_infos, "\n# Views:\n");
+
+	// Go through views and get their infos
+	rewinddir(dms->view_directory);
+	while ((dp = readdir(dms->view_directory)) != NULL)
+	{
+		if ((dp->d_name)[0] == '.')
+			continue;
+		i=0;
+		while ((dp->d_name)[i] != '.')
+			i++;
+		view_name = (char*) malloc((i+1) * sizeof(char));
+		if (view_name == NULL)
+		{
+			obi_set_errno(OBI_MALLOC_ERROR);
+			obidebug(1, "\nError allocating memory for a view name when getting formatted DMS infos: file %s", dp->d_name);
+			return NULL;
+		}
+		strncpy(view_name, dp->d_name, i);
+		view_name[i] = '\0';
+		view = obi_open_view(dms, view_name);
+		if (view == NULL)
+		{
+			obidebug(1, "\nError opening a view to get DMS formatted infos");
+			return NULL;
+		}
+		if (detailed)
+			view_infos = obi_view_formatted_infos(view, detailed);
+		else
+			view_infos = obi_view_formatted_infos_one_line(view);
+		if (view_infos == NULL)
+		{
+			obidebug(1, "\nError getting a view infos to get DMS formatted infos");
+			return NULL;
+		}
+		dms_infos = realloc(dms_infos, (strlen(dms_infos)+strlen(view_infos)+1) * sizeof(char));
+		if (dms_infos == NULL)
+		{
+			obidebug(1, "\nError reallocating memory for DMS formatted infos");
+			return NULL;
+		}
+		strcat(dms_infos, view_infos);
+		if (obi_save_and_close_view(view) < 0)
+		{
+			obidebug(1, "\nError closing view while getting DMS formatted infos");
+			return NULL;
+		}
+		if (detailed)
+		{
+			dms_infos = realloc(dms_infos, (strlen(dms_infos)+2) * sizeof(char));
+			strcat(dms_infos, "\n");
+		}
+	}
+
+	// Add taxonomies
+	dms_infos = realloc(dms_infos, (strlen(dms_infos)+strlen("\n# Taxonomies:\n")+1) * sizeof(char));
+	if (dms_infos == NULL)
+	{
+		obidebug(1, "\nError reallocating memory for DMS formatted infos");
+		return NULL;
+	}
+	strcat(dms_infos, "# Taxonomies:\n");
+	rewinddir(dms->tax_directory);
+	while ((dp = readdir(dms->tax_directory)) != NULL)
+	{
+		if ((dp->d_name)[0] == '.')
+			continue;
+		tax_name = dp->d_name;
+		dms_infos = realloc(dms_infos, (strlen(dms_infos)+strlen("  # ")+strlen(view_infos)+1) * sizeof(char));
+		if (dms_infos == NULL)
+		{
+			obidebug(1, "\nError reallocating memory for DMS formatted infos");
+			return NULL;
+		}
+		strcat(dms_infos, "  # ");
+		strcat(dms_infos, tax_name);
+	}
+	return dms_infos;
+}
+
+
 // TODO move somewhere else maybe
 // TODO discuss arguments
 obiversion_t obi_import_column(const char* dms_path_1, const char* dms_path_2, const char* column_name, obiversion_t version_number)
@@ -1490,7 +1597,7 @@ obiversion_t obi_import_column(const char* dms_path_1, const char* dms_path_2, c
 	memcpy(column_2->data, column_1->data, header_1->data_size);
 
 	// Copy the AVL files if there are some (overwriting the automatically created files)
-	if ((header_1->returned_data_type == OBI_STR) || (header_1->returned_data_type == OBI_SEQ) || (header_1->returned_data_type == OBI_QUAL))
+	if ((header_1->tuples) || ((header_1->returned_data_type == OBI_STR) || (header_1->returned_data_type == OBI_SEQ) || (header_1->returned_data_type == OBI_QUAL)))
 	{
 		avl_name_1 = (char*) malloc((strlen(header_1->indexer_name) + 1)  * sizeof(char));
 		if (avl_name_1 == NULL)
@@ -1653,6 +1760,12 @@ int obi_import_view(const char* dms_path_1, const char* dms_path_2, const char*
 	else	// Non-typed view
 		view_2 = obi_new_view(dms_2, view_name_2, NULL, NULL, (view_1->infos)->comments);
 
+	if (view_2 == NULL)
+	{
+		obidebug(1, "\nError creating the new view to import a view in a DMS");
+		return -1;
+	}
+
 	// Import line count
 	view_2->infos->line_count = view_1->infos->line_count;
 

src/obidms.h

@@ -459,6 +459,23 @@ char* obi_dms_get_full_path(OBIDMS_p dms, const char* path_name);
 DIR* opendir_in_dms(OBIDMS_p dms, const char* path_name);
 
 
+/**
+ * @brief Returns the informations of a DMS with a human readable format (dms name, taxonomies and view infos).
+ *
+ * @warning The returned pointer has to be freed by the caller.
+ *
+ * @param column A pointer on a DMS.
+ * @param detailed Whether the informations should contain detailed view infos.
+ *
+ * @returns A pointer on a character array where the formatted DMS informations are stored.
+ * @retval NULL if an error occurred.
+ *
+ * @since September 2020
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+char* obi_dms_formatted_infos(OBIDMS_p dms, bool detailed);
+
+
 /**
  * @brief Imports a column, copying it from a DMS to another DMS, and returns the version of the column in the destination DMS.
  *

src/obidms_taxonomy.c

@@ -2376,9 +2376,10 @@ int read_merged_dmp(const char* taxdump, OBIDMS_taxonomy_p tax, int32_t* delnode
 				// and the deleted taxids with no current reference. An element of the list is composed of the taxid, and the index
 				// of the taxon in the taxa structure, or -1 for deleted taxids.
 				// Creating the merged list requires to merge the 3 ordered lists into one.
-				while (((nT < (tax->taxa)->count) && ((tax->taxa)->taxon[nT].taxid < old_taxid)) || ((nD >= 0) && (delnodes[nD] < old_taxid)))
+				while (((nT < (tax->taxa)->count) && ((tax->taxa)->taxon[nT].taxid < old_taxid)) ||
+						((nD >= 0) && (delnodes[nD] < old_taxid)))
 				{
-					if ((tax->taxa)->taxon[nT].taxid < delnodes[nD])
+					if ((nT < (tax->taxa)->count) && (tax->taxa)->taxon[nT].taxid < delnodes[nD])
 					{ // Add element from taxa list
 						// Enlarge structure if needed
 						if (n == buffer_size)
@@ -2401,7 +2402,7 @@ int read_merged_dmp(const char* taxdump, OBIDMS_taxonomy_p tax, int32_t* delnode
 						nT++;
 						n++;
 					}
-					else if (delnodes[nD] < (tax->taxa)->taxon[nT].taxid)
+					else
 					{ // Add element from deleted taxids list
 						// Enlarge structure if needed
 						if (n == buffer_size)
@@ -3036,12 +3037,12 @@ OBIDMS_taxonomy_p obi_read_taxonomy(OBIDMS_p dms, const char* taxonomy_name, boo
 
 	strcpy(tax->tax_name, taxonomy_name);
 
-	buffer_size = 2048;
-
 	taxonomy_path = get_taxonomy_path(dms, taxonomy_name);
 	if (taxonomy_path == NULL)
 		return NULL;
 
+	buffer_size = strlen(taxonomy_path) + strlen(taxonomy_name) + 6;
+
 	// Read ranks
 	ranks_file_name = (char*) malloc(buffer_size*sizeof(char));
 	if (ranks_file_name == NULL)
@@ -3648,6 +3649,18 @@ ecotx_t* obi_taxo_get_taxon_with_taxid(OBIDMS_taxonomy_p taxonomy, int32_t taxid
 }
 
 
+char* obi_taxo_get_name_from_name_idx(OBIDMS_taxonomy_p taxonomy, int32_t idx)
+{
+	return (((taxonomy->names)->names)[idx]).name;
+}
+
+
+ecotx_t* obi_taxo_get_taxon_from_name_idx(OBIDMS_taxonomy_p taxonomy, int32_t idx)
+{
+	return (((taxonomy->names)->names)[idx]).taxon;
+}
+
+
 int obi_taxo_is_taxon_under_taxid(ecotx_t* taxon, int32_t other_taxid)		// TODO discuss that this doesn't work with deprecated taxids
 {
 	ecotx_t* next_parent;

src/obidms_taxonomy.h

@@ -447,8 +447,51 @@ ecotx_t* obi_taxo_get_superkingdom(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy);
 const char* obi_taxo_rank_index_to_label(int32_t rank_idx, ecorankidx_t* ranks);
 
 
-// TODO
+/**
+ * @brief Function checking whether a taxid is included in a subset of the taxonomy.
+ *
+ * @param taxonomy A pointer on the taxonomy structure.
+ * @param restrict_to_taxids An array of taxids. The researched taxid must be under at least one of those array taxids.
+ * @param count Number of taxids in restrict_to_taxids.
+ * @param taxid The taxid to check.
+ *
+ * @returns A value indicating whether the taxid is included in the chosen subset of the taxonomy.
+ * @retval 0 if the taxid is not included in the subset of the taxonomy.
+ * @retval 1 if the taxid is included in the subset of the taxonomy.
+ *
+ * @since October 2020
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
 int obi_taxo_is_taxid_included(OBIDMS_taxonomy_p taxonomy,
 			     			   int32_t* restrict_to_taxids,
 				    		   int32_t count,
 					    	   int32_t taxid);
+
+
+/**
+ * @brief Function returning the name of a taxon from its index in the taxonomy name index (econameidx_t).
+ *
+ * @param taxonomy A pointer on the taxonomy structure.
+ * @param idx The index at which the name is in the taxonomy name index (econameidx_t).
+ *
+ * @returns The taxon name.
+ *
+ * @since October 2020
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+char* obi_taxo_get_name_from_name_idx(OBIDMS_taxonomy_p taxonomy, int32_t idx);
+
+
+/**
+ * @brief Function returning a taxon structure from its index in the taxonomy name index (econameidx_t).
+ *
+ * @param taxonomy A pointer on the taxonomy structure.
+ * @param idx The index at which the taxon is in the taxonomy name index (econameidx_t).
+ *
+ * @returns The taxon structure.
+ *
+ * @since October 2020
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+ecotx_t* obi_taxo_get_taxon_from_name_idx(OBIDMS_taxonomy_p taxonomy, int32_t idx);
+

src/obidmscolumn.c

@@ -1312,19 +1312,10 @@ OBIDMS_column_p obi_create_column(OBIDMS_p     dms,
 		return NULL;
 	}
 
-	// Store the associated column reference if needed // TODO discuss cases
-	if (data_type == OBI_QUAL)
+	// Store the associated column reference if needed
+	if ((associated_column_name != NULL) && (*associated_column_name != '\0'))
 	{
-		if ((associated_column_name == NULL) || (*associated_column_name == '\0'))
-		{
-			obidebug(1, "\nError: The name of the associated column when creating a new column is NULL");
-			munmap(new_column->header, header_size);
-			close(column_file_descriptor);
-			free(new_column);
-			return NULL;
-		}
 		strcpy((header->associated_column).column_name, associated_column_name);
-
 		if (associated_column_version == -1)
 		{
 			obidebug(1, "\nError: The version of the associated column when creating a new column is not defined");
@@ -1336,6 +1327,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p     dms,
 		(header->associated_column).version = associated_column_version;
 	}
 
+
 	// If the data type is OBI_STR, OBI_SEQ or OBI_QUAL, the associated obi_indexer is opened or created
 	if ((returned_data_type == OBI_STR) || (returned_data_type == OBI_SEQ) || (returned_data_type == OBI_QUAL) || tuples)
 	{
@@ -1350,6 +1342,8 @@ OBIDMS_column_p obi_create_column(OBIDMS_p     dms,
 		}
 		strncpy(header->indexer_name, final_indexer_name, INDEXER_MAX_NAME);
 	}
+	else
+		new_column->indexer = NULL;
 
 	// Fill the data with NA values
 	obi_ini_to_NA_values(new_column, 0, nb_lines);
@@ -1558,6 +1552,8 @@ OBIDMS_column_p obi_open_column(OBIDMS_p     dms,
 			return NULL;
 		}
 	}
+	else
+		column->indexer = NULL;
 
 	if (close(column_file_descriptor) < 0)
 	{
@@ -1693,8 +1689,8 @@ int obi_close_column(OBIDMS_column_p column)
 		if (obi_dms_unlist_column(column->dms, column) < 0)
 			ret_val = -1;
 
-		// If the data type is OBI_STR, OBI_SEQ or OBI_QUAL, the associated indexer is closed
-		if (((column->header)->returned_data_type == OBI_STR) || ((column->header)->returned_data_type == OBI_SEQ) || ((column->header)->returned_data_type == OBI_QUAL))
+		// If it's a tuple column or the data type is OBI_STR, OBI_SEQ or OBI_QUAL, the associated indexer is closed
+		if ((column->indexer) != NULL)
 			if (obi_close_indexer(column->indexer) < 0)
 				ret_val = -1;
 
@@ -1729,16 +1725,32 @@ int obi_close_column(OBIDMS_column_p column)
 int obi_clone_column_indexer(OBIDMS_column_p column)
 {
 	char* new_indexer_name;
+	int i;
 
-	new_indexer_name = obi_build_indexer_name((column->header)->name, (column->header)->version);
-	if (new_indexer_name == NULL)
-		return -1;
-
-	column->indexer = obi_clone_indexer(column->indexer, new_indexer_name);	// TODO Need to lock this somehow?
-	if (column->indexer == NULL)
+	i=0;
+	while (true) // find avl name not already used
 	{
-		obidebug(1, "\nError cloning a column's indexer to make it writable");
-		return -1;
+		new_indexer_name = obi_build_indexer_name((column->header)->name, ((column->header)->version)+i);
+		if (new_indexer_name == NULL)
+			return -1;
+
+		column->indexer = obi_clone_indexer(column->indexer, new_indexer_name);	// TODO Need to lock this somehow?
+		if (column->indexer == NULL)
+		{
+			if (errno == EEXIST)
+			{
+				free(new_indexer_name);
+				i++;
+			}
+			else
+			{
+				free(new_indexer_name);
+				obidebug(1, "\nError cloning a column's indexer to make it writable");
+				return -1;
+			}
+		}
+		else
+			break;
 	}
 
 	strcpy((column->header)->indexer_name, new_indexer_name);
@@ -1973,7 +1985,11 @@ int obi_enlarge_column(OBIDMS_column_p column)
 
 	// Calculate the new file size
 	old_line_count = (column->header)->line_count;
-	new_line_count = old_line_count * COLUMN_GROWTH_FACTOR;
+	new_line_count = ceil((double) old_line_count * (double) COLUMN_GROWTH_FACTOR);
+	if (new_line_count > old_line_count+100000)
+		new_line_count = old_line_count+100000;
+	else if (new_line_count < old_line_count+1000)
+		new_line_count = old_line_count+1000;
 
 	if (new_line_count > MAXIMUM_LINE_COUNT)
 	{
@@ -2381,6 +2397,118 @@ char* obi_get_elements_names(OBIDMS_column_p column)
 }
 
 
+char* obi_get_formatted_elements_names(OBIDMS_column_p column)
+{
+	char* elements_names;
+	int   i, j;
+	int   elt_idx;
+	int   len;
+
+	elements_names = (char*) malloc(((column->header)->elements_names_length + (column->header)->nb_elements_per_line) * sizeof(char));
+	if (elements_names == NULL)
+	{
+		obi_set_errno(OBI_MALLOC_ERROR);
+		obidebug(1, "\nError allocating memory for elements names");
+		return NULL;
+	}
+
+	j = 0;
+	for (i=0; i < (column->header)->nb_elements_per_line; i++)
+	{
+		elt_idx = ((column->header)->elements_names_idx)[i];
+		len = strlen(((column->header)->elements_names)+elt_idx);
+		memcpy(elements_names+j, ((column->header)->elements_names)+elt_idx, len*sizeof(char));
+		j = j + len;
+		elements_names[j] = ';';
+		j++;
+		elements_names[j] = ' ';
+		j++;
+	}
+
+	elements_names[j - 1] = '\0';
+
+	return elements_names;
+}
+
+
+char* obi_column_formatted_infos(OBIDMS_column_p column, bool detailed)
+{
+	char* column_infos = NULL;
+	char* elt_names = NULL;
+	char* data_type_str = NULL;
+	char* comments = NULL;
+
+	// Get element names informations
+	elt_names = obi_get_formatted_elements_names(column);
+	if (elt_names == NULL)
+	{
+		obidebug(1, "\nError getting formatted elements names for formatted columns infos");
+		return NULL;
+	}
+
+	// Get data type informations
+	data_type_str = name_data_type((column->header)->returned_data_type);
+	if (data_type_str == NULL)
+	{
+		obidebug(1, "\nError getting formatted data type for formatted columns infos");
+		return NULL;
+	}
+
+	// Get commments if detailed informations required
+	if (detailed)
+		comments = (column->header)->comments;
+
+	// Build the string of formatted infos, allocating memory as needed
+
+	// Data type
+	column_infos = (char*) malloc((strlen("data type: ")+strlen(data_type_str)+1) * sizeof(char));
+	if (column_infos == NULL)
+	{
+		obi_set_errno(OBI_MALLOC_ERROR);
+		obidebug(1, "\nError allocating memory for formatted column infos");
+		return NULL;
+	}
+
+	strcpy(column_infos, "data type: ");
+	strcat(column_infos, data_type_str);
+
+	// Element names if more than 1
+	if ((column->header)->nb_elements_per_line > 1)
+	{
+		column_infos = realloc(column_infos, (strlen(column_infos)+strlen(", elements: ")+strlen(elt_names)+1) * sizeof(char));
+		if (column_infos == NULL)
+		{
+			obi_set_errno(OBI_MALLOC_ERROR);
+			obidebug(1, "\nError allocating memory for formatted column infos");
+			return NULL;
+		}
+
+		strcat(column_infos, ", elements: ");
+		strcat(column_infos, elt_names);
+	}
+
+	if (detailed && (strlen(comments)>2)) // Add all comments if required and not empty
+	{
+		column_infos = realloc(column_infos, (strlen(column_infos)+strlen("\nComments:\n")+strlen(comments)+1) * sizeof(char));
+		if (column_infos == NULL)
+		{
+			obi_set_errno(OBI_MALLOC_ERROR);
+			obidebug(1, "\nError allocating memory for formatted column infos");
+			return NULL;
+		}
+
+		strcat(column_infos, "\nComments:\n");
+		strcat(column_infos, comments);
+	}
+
+//  "data type: OBI_TYPE, element names: [formatted element names](, all comments)"
+
+	free(elt_names);
+	free(data_type_str);
+
+	return column_infos;
+}
+
 
 int obi_column_prepare_to_set_value(OBIDMS_column_p column, index_t line_nb, index_t elt_idx)
 {
@@ -2424,7 +2552,6 @@ int obi_column_prepare_to_set_value(OBIDMS_column_p column, index_t line_nb, ind
 }
 
 
-
 int obi_column_prepare_to_get_value(OBIDMS_column_p column, index_t line_nb)
 {
 	if ((line_nb+1) > ((column->header)->line_count))

src/obidmscolumn.h

@@ -505,6 +505,39 @@ index_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const cha
 char* obi_get_elements_names(OBIDMS_column_p column);
 
 
+/**
+ * @brief Recovers the elements names of the lines of a column with a human readable format ("0; 1; 2; ...; n\0").
+ *
+ * @warning The returned pointer has to be freed by the caller.
+ *
+ * @param column A pointer on an OBIDMS column.
+ *
+ * @returns A pointer on a character array where the elements names are stored.
+ * @retval NULL if an error occurred.
+ *
+ * @since September 2020
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+char* obi_get_formatted_elements_names(OBIDMS_column_p column);
+
+
+/**
+ * @brief Returns the informations of a column with a human readable format (data type, element names, comments).
+ *
+ * @warning The returned pointer has to be freed by the caller.
+ *
+ * @param column A pointer on an OBIDMS column.
+ * @param detailed Whether the informations should contain column comments or just data type and element names.
+ *
+ * @returns A pointer on a character array where the formatted column informations are stored.
+ * @retval NULL if an error occurred.
+ *
+ * @since September 2020
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+char* obi_column_formatted_infos(OBIDMS_column_p column, bool detailed);
+
+
 /**
  * @brief Prepares a column to set a value.
  *

src/obitypes.h

@@ -34,8 +34,8 @@
  * @brief enum for the boolean OBIType.
  */
 typedef enum OBIBool {
-    FALSE      = 0,
-    TRUE       = 1,
+    OBIFalse   = 0,
+    OBITrue    = 1,
     OBIBool_NA = 2
 } obibool_t, *obibool_p; 		/**< a boolean true/false value */	// TODO check name convention?
 

src/obiview.c

@@ -17,6 +17,7 @@
 #include <sys/mman.h>
 #include <inttypes.h>
 #include <math.h>
+#include <time.h>
 //#include <ctype.h>
 
 #include "obiview.h"
@@ -254,11 +255,15 @@ static int update_lines(Obiview_p view, index_t line_count);
 /**
  * @brief Internal function to clone a column in the context of a view.
  *
+ * Used to edit a closed column.
+ *
  * Clones with the right line selection and replaces the cloned columns with the new ones in the view.
  * If there is a line selection, all columns have to be cloned, otherwise only the column of interest is cloned.
  *
  * @param view A pointer on the view.
  * @param column_name The name of the column in the view that should be cloned.
+ * @param clone_associated Whether to clone the associated column
+ *  	  (should always be true except when calling from the function itself to avoid infinite recursion).
  *
  * @returns A pointer on the new column.
  * @retval NULL if an error occurred.
@@ -266,7 +271,7 @@ static int update_lines(Obiview_p view, index_t line_count);
  * @since February 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-static OBIDMS_column_p clone_column_in_view(Obiview_p view, const char* column_name);
+static OBIDMS_column_p clone_column_in_view(Obiview_p view, const char* column_name, bool clone_associated);
 
 
 /**
@@ -845,7 +850,7 @@ static int update_lines(Obiview_p view, index_t line_count)
 		// Clone the column first if needed
 		if (!(column->writable))
 		{
-			column = clone_column_in_view(view, (((view->infos)->column_references)[i]).alias);
+			column = clone_column_in_view(view, (((view->infos)->column_references)[i]).alias, true);
 			if (column == NULL)
 			{
 				obidebug(1, "\nError cloning a column in a view when updating its line count");
@@ -870,12 +875,14 @@ static int update_lines(Obiview_p view, index_t line_count)
 }
 
 
-static OBIDMS_column_p clone_column_in_view(Obiview_p view, const char* column_name)
+static OBIDMS_column_p clone_column_in_view(Obiview_p view, const char* column_name, bool clone_associated)
 {
-	int i;
+	int i, j;
 	OBIDMS_column_p column = NULL;
 	OBIDMS_column_p new_column = NULL;
 	OBIDMS_column_p column_buffer;
+	OBIDMS_column_p associated_cloned_column = NULL;
+	char* associated_column_alias = NULL;
 
 	// Check that the view is not read-only
 	if (view->read_only)
@@ -916,11 +923,62 @@ static OBIDMS_column_p clone_column_in_view(Obiview_p view, const char* column_n
 				return NULL;
 			}
 
+			// Look for associated column to clone and reassociate
+			if ((column_buffer->header->associated_column).column_name[0] != '\0')
+			{
+				// Get the associated column alias
+				j=0;
+				while (((strcmp((((view->infos)->column_references)[j]).column_refs.column_name, (column_buffer->header->associated_column).column_name)) ||
+						((((view->infos)->column_references)[j]).column_refs.version != (column_buffer->header->associated_column).version)) &&
+						j<(view->infos)->column_count)  // TODO function for that
+					j++;
+
+				if (j == (view->infos)->column_count) // not found
+				{
+					obi_set_errno(OBIVIEW_ERROR);
+					obidebug(1, "\nCould not find associated column when cloning a column for editing");
+					return NULL;
+				}
+
+				// No line selection: only this column is cloned, clone and reassociate the associated column
+				if ((view->line_selection == NULL) && clone_associated)
+				{
+					associated_column_alias = (((view->infos)->column_references)[j]).alias;
+					// Clone the associated column
+					associated_cloned_column = clone_column_in_view(view, associated_column_alias, false);
+					// Reassociate both ways
+					strcpy((associated_cloned_column->header->associated_column).column_name, column->header->name);
+					(associated_cloned_column->header->associated_column).version = column->header->version;
+					strcpy((column->header->associated_column).column_name, associated_cloned_column->header->name);
+					(column->header->associated_column).version = associated_cloned_column->header->version;
+				}
+				else
+				{
+					// Line selection: all columns are cloned, check if associated column has been cloned previously (it precedes this one in the list) to reassociate
+					if (j < i)
+					{
+						// Get pointer to associated column
+						associated_cloned_column = *((OBIDMS_column_p*)ll_get(view->columns, j));
+						if (associated_cloned_column == NULL)
+						{
+							obi_set_errno(OBIVIEW_ERROR);
+							obidebug(1, "\nError getting a column to clone from the linked list of column pointers of a view");
+							return NULL;
+						}
+						// Reassociate both ways
+						strcpy((associated_cloned_column->header->associated_column).column_name, column->header->name);
+						(associated_cloned_column->header->associated_column).version = column->header->version;
+						strcpy((column->header->associated_column).column_name, associated_cloned_column->header->name);
+						(column->header->associated_column).version = associated_cloned_column->header->version;
+					}
+				}
+			}
+
 			// Close old cloned column
 			obi_close_column(column_buffer);
 
 			if (!strcmp((((view->infos)->column_references)[i]).alias, column_name))
-				// Found the column to return
+				// Get the column to return
 				new_column = column;
 		}
 	}
@@ -1037,8 +1095,9 @@ static int finish_view(Obiview_p view)
 		return -1;
 	}
 
-	// Add count column if it's a NUC_SEQ_VIEW with no count column // TODO discuss
-	if ((!strcmp((view->infos)->view_type, VIEW_TYPE_NUC_SEQS)) && (!obi_view_column_exists(view, COUNT_COLUMN)))
+	// Add count column if it's a NUC_SEQ_VIEW with no count column (and there's no MERGED_sample column) // TODO discuss
+	if ((!strcmp((view->infos)->view_type, VIEW_TYPE_NUC_SEQS)) && (!obi_view_column_exists(view, COUNT_COLUMN))
+			&& (!obi_view_column_exists(view, "MERGED_sample")))  // TODO should eventually compute from merged samples?
 	{
 		if (obi_create_auto_count_column(view) < 0)
 		{
@@ -1127,6 +1186,7 @@ static int close_view(Obiview_p view)
 			obidebug(1, "\nError getting a column to close from the linked list of column pointers of a view");
 			return -1;
 		}
+
 		if (obi_close_column(column) < 0)
 		{
 			obidebug(1, "\nError closing a column while closing a view");
@@ -1192,7 +1252,7 @@ static int prepare_to_set_value_in_column(Obiview_p view, OBIDMS_column_p* colum
 			return -1;
 		}
 
-		(*column_pp) = clone_column_in_view(view, column_name);
+		(*column_pp) = clone_column_in_view(view, column_name, true);
 		if ((*column_pp) == NULL)
 		{
 			obidebug(1, "\nError trying to clone a column to modify it");
@@ -1407,7 +1467,7 @@ static char* view_check_qual_match_seqs(Obiview_p view)
 						// Test that the lengths of the quality and the sequence are equal
 						if ((size_t)qual_len != strlen(seq))
 						{
-							obidebug(1, "\nError checking the predicate for view %s: The sequences and sequence quality arrays match.", (view->infos)->name);
+							obidebug(1, "\nError checking the predicate for view %s: The sequences and sequence quality arrays match (index %lld, seq=%s, quality length = %d).", (view->infos)->name, j, seq, qual_len);
 							return NULL;
 						}
 					}
@@ -1843,6 +1903,7 @@ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p v
 {
 	Obiview_p 		view;
 	OBIDMS_column_p associated_nuc_column;
+	OBIDMS_column_p associated_qual_column;
 	int				nb_predicates;
 
 	if (view_to_clone != NULL)
@@ -1895,6 +1956,10 @@ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p v
 				obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
 				return NULL;
 			}
+			// Associating both ways: associating nuc sequences column to quality column
+			associated_qual_column = obi_view_get_column(view, QUALITY_COLUMN);
+			strcpy((associated_nuc_column->header->associated_column).column_name, associated_qual_column->header->name);
+			(associated_nuc_column->header->associated_column).version = associated_qual_column->header->version;
 		}
 	}
 
@@ -1921,7 +1986,7 @@ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p v
 	(view->predicate_functions)[(view->nb_predicates)] = view_has_nuc_sequence_column;
 	(view->predicate_functions)[(view->nb_predicates) + 1] = view_has_id_column;
 	(view->predicate_functions)[(view->nb_predicates) + 2] = view_has_definition_column;
-//	if (quality_column)   # TODO discuss. Commented bc for example with obi annotate, clone view so clone predicate, then modify seq, so quality is deleted, and predicate boom
+//	if (quality_column)   # TODO fix by triggering predicate deleting if quality deleting. Commented bc for example with obi annotate, clone view so clone predicate, then modify seq, so quality is deleted, and predicate boom
 //		(view->predicate_functions)[(view->nb_predicates) + 3] = view_has_quality_column;
 
 	view->nb_predicates = nb_predicates;
@@ -2211,7 +2276,7 @@ Obiview_p obi_open_view(OBIDMS_p dms, const char* view_name)
 
 // TODO return a pointer on the column?
 int obi_view_add_column(Obiview_p    view,
-						char*  column_name,
+						char*        column_name,
 						obiversion_t version_number,
 						const char*  alias,
 						OBIType_t    data_type,
@@ -2380,11 +2445,12 @@ int obi_view_add_column(Obiview_p    view,
 }
 
 
-int obi_view_delete_column(Obiview_p view, const char* column_name)
+int obi_view_delete_column(Obiview_p view, const char* column_name, bool delete_file)
 {
 	int  i;
 	bool found;
 	OBIDMS_column_p column;
+	char* col_to_delete_path;
 
 	// Check that the view is not read-only
 	if (view->read_only)
@@ -2406,8 +2472,31 @@ int obi_view_delete_column(Obiview_p view, const char* column_name)
 				obidebug(1, "\nError getting a column from the linked list of column pointers of a view when deleting a column from a view");
 				return -1;
 			}
+			// Keep column path if need to delete the file
+			if (delete_file)
+			{
+				col_to_delete_path = obi_column_full_path(view->dms, column->header->name, column->header->version);
+				if (col_to_delete_path == NULL)
+				{
+					obidebug(1, "\nError getting a column file path when deleting a column");
+					return -1;
+				}
+			}
 
 			obi_close_column(column);
+
+			// Delete file if needed
+			if (delete_file)
+			{
+				if (remove(col_to_delete_path) < 0)
+				{
+					obi_set_errno(OBICOL_UNKNOWN_ERROR);
+					obidebug(1, "\nError deleting a column file when deleting unfinished columns: file %s", col_to_delete_path);
+					return -1;
+				}
+				free(col_to_delete_path);
+			}
+
 			view->columns = ll_delete(view->columns, i);
 			// TODO how do we check for error? NULL can be empty list
 			found = true;
@@ -2516,6 +2605,144 @@ int obi_view_create_column_alias(Obiview_p view, const char* current_name, const
 }
 
 
+char* obi_view_formatted_infos(Obiview_p view, bool detailed)
+{
+	int             i;
+	char*   		view_infos = NULL;
+	char*   		view_name = NULL;
+	time_t  		creation_date;
+	char*			creation_date_str = NULL;
+	index_t 		line_count;
+	char    		line_count_str[256];
+	OBIDMS_column_p column;
+	char*			column_alias = NULL;
+	char*   		column_infos = NULL;
+	char*			comments = NULL;
+
+	// View name
+	view_name = (view->infos)->name;
+	view_infos = (char*) malloc((strlen("# View name:\n")+strlen(view_name)+1) * sizeof(char));
+	strcpy(view_infos, "# View name:\n");
+	strcat(view_infos, view_name);
+
+	// Date created
+	if (view->read_only) // Date not saved until view is finished writing
+	{
+		creation_date = (view->infos)->creation_date;
+		creation_date_str = ctime(&creation_date);
+		view_infos = realloc(view_infos, (strlen(view_infos)+strlen("\n# Date created:\n")+strlen(creation_date_str)+1) * sizeof(char));
+		strcat(view_infos, "\n# Date created:\n");
+		strcat(view_infos, creation_date_str);
+	}
+
+	// Line count
+	line_count = (view->infos)->line_count;
+	snprintf(line_count_str, sizeof line_count_str, "%lld", line_count);
+	view_infos = realloc(view_infos, (strlen(view_infos)+strlen("\n# Line count:\n")+strlen(line_count_str)+1) * sizeof(char));
+	strcat(view_infos, "# Line count:\n");
+	strcat(view_infos, line_count_str);
+
+	// Columns: go through each, print their alias then their infos
+	view_infos = realloc(view_infos, (strlen(view_infos)+strlen("\n# Columns:")+1) * sizeof(char));
+	strcat(view_infos, "\n# Columns:");
+	for (i=0; i<((view->infos)->column_count); i++)
+	{
+		column = *((OBIDMS_column_p*)ll_get(view->columns, i));
+		if (column == NULL)
+		{
+			obidebug(1, "\nError getting a column from the linked list of column pointers of a view to format view infos");
+			return NULL;
+		}
+
+		// Column alias
+		column_alias = (((view->infos)->column_references)[i]).alias;
+		view_infos = realloc(view_infos, (strlen(view_infos)+strlen("\n")+strlen(column_alias)+strlen(", ")+1) * sizeof(char));
+		strcat(view_infos, "\n");
+		strcat(view_infos, column_alias);
+		strcat(view_infos, ", ");
+
+		// Column infos
+		column_infos = obi_column_formatted_infos(column, detailed);
+		if (column_infos == NULL)
+		{
+			obidebug(1, "\nError getting column infos to format view infos");
+			return NULL;
+		}
+
+		view_infos = realloc(view_infos, (strlen(view_infos)+strlen(column_infos)+1) * sizeof(char));
+		strcat(view_infos, column_infos);
+		free(column_infos);
+	}
+
+	// Get commments if detailed informations required
+	if (detailed)
+	{
+		comments = (view->infos)->comments;
+		if (strlen(comments)>2) // Add all comments if not empty
+		{
+			view_infos = realloc(view_infos, (strlen(view_infos)+strlen("\n# Comments:\n")+strlen(comments)+1) * sizeof(char));
+			if (view_infos == NULL)
+			{
+				obi_set_errno(OBI_MALLOC_ERROR);
+				obidebug(1, "\nError allocating memory for formatted view infos");
+				return NULL;
+			}
+
+			strcat(view_infos, "\n# Comments:\n");
+			strcat(view_infos, comments);
+		}
+	}
+
+	view_infos = realloc(view_infos, (strlen(view_infos)+2) * sizeof(char));
+	strcat(view_infos, "\n");
+
+	return view_infos;
+}
+
+
+char* obi_view_formatted_infos_one_line(Obiview_p view)
+{
+	int             i;
+	char*   		view_infos = NULL;
+	char*   		view_name = NULL;
+	time_t  		creation_date;
+	char*			creation_date_str = NULL;
+	index_t 		line_count;
+	char    		line_count_str[256];
+
+	// View name
+	view_name = (view->infos)->name;
+	view_infos = (char*) malloc((strlen("  # ")+strlen(view_name)+2) * sizeof(char));
+	strcpy(view_infos, "  # ");
+	strcat(view_infos, view_name);
+	strcat(view_infos, ":");
+
+	// Date created
+	if (view->read_only) // Date not saved until view is finished writing
+	{
+		creation_date = (view->infos)->creation_date;
+		creation_date_str = ctime(&creation_date);
+		// Delete \n added by ctime
+		creation_date_str[strlen(creation_date_str)-1] = '\0';
+		view_infos = realloc(view_infos, (strlen(view_infos)+strlen(" Date created: ")+strlen(creation_date_str)+1) * sizeof(char));
+		strcat(view_infos, " Date created: ");
+		strcat(view_infos, creation_date_str);
+	}
+
+	// Line count
+	line_count = (view->infos)->line_count;
+	snprintf(line_count_str, sizeof line_count_str, "%lld", line_count);
+	view_infos = realloc(view_infos, (strlen(view_infos)+strlen(" ; Line count: ")+strlen(line_count_str)+1) * sizeof(char));
+	strcat(view_infos, " ; Line count: ");
+	strcat(view_infos, line_count_str);
+
+	view_infos = realloc(view_infos, (strlen(view_infos)+2) * sizeof(char));
+	strcat(view_infos, "\n");
+
+	return view_infos;
+}
+
+
 int obi_view_write_comments(Obiview_p view, const char* comments)
 {
 	size_t new_size;
@@ -3047,7 +3274,7 @@ int obi_create_auto_id_column(Obiview_p view, const char* prefix)
 	// Delete old ID column if it exists
 	if (obi_view_get_column(view, ID_COLUMN) != NULL)
 	{
-		if (obi_view_delete_column(view, ID_COLUMN) < 0)
+		if (obi_view_delete_column(view, ID_COLUMN, false) < 0)
 		{
 			obidebug(1, "Error deleting an ID column to replace it in a view");
 			return -1;

src/obiview.h

@@ -30,45 +30,56 @@
 #include "obiblob.h"
 
 
-#define OBIVIEW_NAME_MAX_LENGTH (249)   		/**< The maximum length of an OBIDMS view name, without the extension.
-                                	 	  	  	 */
-#define VIEW_TYPE_MAX_LENGTH (1024)   			/**< The maximum length of the type name of a view.
-                                	 	  	  	 */
-#define LINES_COLUMN_NAME "LINES"				/**< The name of the column containing the line selections
- 	 	 	 	 	 	 	 	 	 	 	 	 *   in all views.
-                                	 	  	  	 */
-#define VIEW_TYPE_NUC_SEQS "NUC_SEQS_VIEW"   	/**< The type name of views based on nucleotide sequences
-												 *   and their metadata.
-                                	 	  	  	 */
-#define NUC_SEQUENCE_COLUMN "NUC_SEQ"			/**< The name of the column containing the nucleotide sequences
- 	 	 	 	 	 	 	 	 	 	 	 	 *   in NUC_SEQS_VIEW views.
-                                	 	  	  	 */
-#define ID_COLUMN "ID"							/**< The name of the column containing the sequence identifiers
- 	 	 	 	 	 	 	 	 	 	 	 	 *   in NUC_SEQS_VIEW views.
-                                	 	  	  	 */
-#define DEFINITION_COLUMN "DEFINITION"			/**< The name of the column containing the sequence definitions
- 	 	 	 	 	 	 	 	 	 	 	 	 *   in NUC_SEQS_VIEW views.
-                                	 	  	  	 */
-#define QUALITY_COLUMN "QUALITY"				/**< The name of the column containing the sequence qualities
- 	 	 	 	 	 	 	 	 	 	 	 	 *   in NUC_SEQS_VIEW views.
-                                	 	  	   	 */
-#define COUNT_COLUMN "COUNT"				    /**< The name of the column containing the sequence counts
- 	 	 	 	 	 	 	 	 	 	 	 	 *   in NUC_SEQS_VIEW views.
-                                	 	  	  	 */
-#define TAXID_COLUMN "TAXID"				    /**< The name of the column containing the taxids.       TODO subtype of INT column?
-                                	             */
-#define MERGED_TAXID_COLUMN "MERGED_TAXID"		/**< The name of the column containing the merged taxids information.
-                                	             */
-#define MERGED_PREFIX "MERGED_"		            /**< The prefix to prepend to column names when merging informations during obi uniq.
-                                	             */
-#define TAXID_DIST_COLUMN "TAXID_DIST"			/**< The name of the column containing a dictionary of taxid:[list of ids] when merging informations during obi uniq.
-                                	             */
-#define MERGED_COLUMN "MERGED"					/**< The name of the column containing a list of ids when merging informations during obi uniq.
-                                	             */
-#define ID_PREFIX "seq"						    /**< The default prefix of sequence identifiers in automatic ID columns.
-                                	 	  	  	 */
-#define PREDICATE_KEY "predicates"		        /**< The key used in the json-formatted view comments to store predicates.
-                                	 	  	  	 */
+#define OBIVIEW_NAME_MAX_LENGTH (249)   		   /**< The maximum length of an OBIDMS view name, without the extension.
+                                	 	  	  	    */
+#define VIEW_TYPE_MAX_LENGTH (1024)   			   /**< The maximum length of the type name of a view.
+                                	 	  	  	    */
+#define LINES_COLUMN_NAME "LINES"				   /**< The name of the column containing the line selections
+ 	 	 	 	 	 	 	 	 	 	 	 	    *   in all views.
+                                	 	  	  	    */
+#define VIEW_TYPE_NUC_SEQS "NUC_SEQS_VIEW"   	   /**< The type name of views based on nucleotide sequences
+												    *   and their metadata.
+                                	 	  	  	    */
+#define NUC_SEQUENCE_COLUMN "NUC_SEQ"			   /**< The name of the column containing the nucleotide sequences
+ 	 	 	 	 	 	 	 	 	 	 	 	    *   in NUC_SEQS_VIEW views.
+                                	 	  	  	    */
+#define ID_COLUMN "ID"							   /**< The name of the column containing the sequence identifiers
+ 	 	 	 	 	 	 	 	 	 	 	 	    *   in NUC_SEQS_VIEW views.
+                                	 	  	  	    */
+#define DEFINITION_COLUMN "DEFINITION"			   /**< The name of the column containing the sequence definitions
+ 	 	 	 	 	 	 	 	 	 	 	 	    *   in NUC_SEQS_VIEW views.
+                                	 	  	  	    */
+#define QUALITY_COLUMN "QUALITY"				   /**< The name of the column containing the sequence qualities
+ 	 	 	 	 	 	 	 	 	 	 	 	    *   in NUC_SEQS_VIEW views.
+                                	 	  	   	    */
+#define REVERSE_QUALITY_COLUMN "REVERSE_QUALITY"   /**< The name of the column containing the sequence qualities
+ 	 	 	 	 	 	 	 	 	 	 	 	    *    of the reverse read (generated by ngsfilter, used by alignpairedend).
+                                	 	  	   	    */
+#define REVERSE_SEQUENCE_COLUMN "REVERSE_SEQUENCE" /**< The name of the column containing the sequence
+ 	 	 	 	 	 	 	 	 	 	 	 	    *    of the reverse read (generated by ngsfilter, used by alignpairedend).
+                                	 	  	   	    */
+#define QUALITY_COLUMN "QUALITY"				   /**< The name of the column containing the sequence qualities
+ 	 	 	 	 	 	 	 	 	 	 	 	    *   in NUC_SEQS_VIEW views.
+                                	 	  	   	    */
+#define COUNT_COLUMN "COUNT"				       /**< The name of the column containing the sequence counts
+ 	 	 	 	 	 	 	 	 	 	 	 	    *   in NUC_SEQS_VIEW views.
+                                	 	  	  	    */
+#define SCIENTIFIC_NAME_COLUMN "SCIENTIFIC_NAME"   /**< The name of the column containing the taxon scientific name.
+                                	                */
+#define TAXID_COLUMN "TAXID"				       /**< The name of the column containing the taxids.       TODO subtype of INT column?
+                                	                */
+#define MERGED_TAXID_COLUMN "MERGED_TAXID"		   /**< The name of the column containing the merged taxids information.
+                                	                */
+#define MERGED_PREFIX "MERGED_"		               /**< The prefix to prepend to column names when merging informations during obi uniq.
+                                	                */
+#define TAXID_DIST_COLUMN "TAXID_DIST"			   /**< The name of the column containing a dictionary of taxid:[list of ids] when merging informations during obi uniq.
+                                	                */
+#define MERGED_COLUMN "MERGED"					   /**< The name of the column containing a list of ids when merging informations during obi uniq.
+                                	                */
+#define ID_PREFIX "seq"						       /**< The default prefix of sequence identifiers in automatic ID columns.
+                                	 	  	  	    */
+#define PREDICATE_KEY "predicates"		           /**< The key used in the json-formatted view comments to store predicates.
+                                	 	  	  	    */
 
 
 /**
@@ -397,7 +408,7 @@ Obiview_p obi_open_view(OBIDMS_p dms, const char* view_name);
  * @param associated_column_name The name of the associated column if there is one (otherwise NULL or ""), if the column is created.
  * @param associated_column_version The version of the associated column if there is one (otherwise -1), if the column is created.
  * @param comments Optional comments associated with the column if it is created (NULL or "" if no comments associated).
- * @param create Whether the column should be created (create == true) or opened (create == false).
+ * @param create Whether the column should be created (create == true) or already exists (create == false).
  *
  * @returns A value indicating the success of the operation.
  * @retval 0 if the operation was successfully completed.
@@ -407,7 +418,7 @@ Obiview_p obi_open_view(OBIDMS_p dms, const char* view_name);
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
 int obi_view_add_column(Obiview_p    view,
-						char*  column_name,
+						char*        column_name,
 						obiversion_t version_number,
 						const char*  alias,
 						OBIType_t    data_type,
@@ -431,6 +442,7 @@ int obi_view_add_column(Obiview_p    view,
  *
  * @param view A pointer on the view.
  * @param column_name The name of the column that should be deleted from the view.
+ * @param delete_file Whether the column file should be deleted. Use carefully re: dependencies.
  *
  * @returns A value indicating the success of the operation.
  * @retval 0 if the operation was successfully completed.
@@ -439,7 +451,7 @@ int obi_view_add_column(Obiview_p    view,
  * @since February 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_view_delete_column(Obiview_p view, const char* column_name);
+int obi_view_delete_column(Obiview_p view, const char* column_name, bool delete_file);
 
 
 /**
@@ -509,6 +521,39 @@ OBIDMS_column_p* obi_view_get_pointer_on_column_in_view(Obiview_p view, const ch
 int obi_view_create_column_alias(Obiview_p view, const char* current_name, const char* alias);
 
 
+/**
+ * @brief Returns the informations of a view with a human readable format (view name, date created, line count, column informations, comments).
+ *
+ * @warning The returned pointer has to be freed by the caller.
+ *
+ * @param column A pointer on a view.
+ * @param detailed Whether the informations should contain view comments.
+ *
+ * @returns A pointer on a character array where the formatted view informations are stored.
+ * @retval NULL if an error occurred.
+ *
+ * @since September 2020
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+char* obi_view_formatted_infos(Obiview_p view, bool detailed);
+
+
+/**
+ * @brief Returns the informations of a view with a human readable format on one line (view name, date created, line count).
+ *
+ * @warning The returned pointer has to be freed by the caller.
+ *
+ * @param column A pointer on a view.
+ *
+ * @returns A pointer on a character array where the formatted view informations are stored.
+ * @retval NULL if an error occurred.
+ *
+ * @since September 2020
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+char* obi_view_formatted_infos_one_line(Obiview_p view);
+
+
 /**
  * @brief Internal function writing new comments in a view file.
  *

src/sse_banded_LCS_alignment.c

@@ -686,6 +686,9 @@ int calculateSizeToAllocate(int maxLen, int LCSmin)
 	size *=  3;
 	size +=  16;
 
+	size += 10;  // band-aid for memory bug I don't understand (triggered on specific db on ubuntu)
+				 // bug might have to do with the way different systems behave when aligning the address in obi_get_memory_aligned_on_16
+
 	return(size*sizeof(int16_t));
 }
 
@@ -951,15 +954,15 @@ double generic_sse_banded_lcs_align(char* seq1, char* seq2, double threshold, bo
 	// Put the DNA sequences in the int arrays. Longest sequence must be first argument of sse_align function
 	if (l2 > l1)
 	{
-		putSeqInSeq(iseq1, seq2, l2, TRUE);
-		putSeqInSeq(iseq2, seq1, l1, FALSE);
+		putSeqInSeq(iseq1, seq2, l2, true);
+		putSeqInSeq(iseq2, seq1, l1, false);
 		// Compute alignment
 		id = sse_banded_lcs_align(iseq1, iseq2, l2, l1, normalize, reference, similarity_mode, address, LCSmin, lcs_length, ali_length);
 	}
 	else
 	{
-		putSeqInSeq(iseq1, seq1, l1, TRUE);
-		putSeqInSeq(iseq2, seq2, l2, FALSE);
+		putSeqInSeq(iseq1, seq1, l1, true);
+		putSeqInSeq(iseq2, seq2, l2, false);
 		// Compute alignment
 		id = sse_banded_lcs_align(iseq1, iseq2, l1, l2, normalize, reference, similarity_mode, address, LCSmin, lcs_length, ali_length);
 	}
@@ -1054,15 +1057,15 @@ double obiblob_sse_banded_lcs_align(Obi_blob_p seq1, Obi_blob_p seq2, double thr
 	// Put the DNA sequences in the int arrays. Longest sequence must be first argument of sse_align function
 	if (l2 > l1)
 	{
-		putBlobInSeq(iseq1, seq2, l2, TRUE);
-		putBlobInSeq(iseq2, seq1, l1, FALSE);
+		putBlobInSeq(iseq1, seq2, l2, true);
+		putBlobInSeq(iseq2, seq1, l1, false);
 		// Compute alignment
 		id = sse_banded_lcs_align(iseq1, iseq2, l2, l1, normalize, reference, similarity_mode, address, LCSmin, lcs_length, ali_length);
 	}
 	else
 	{
-		putBlobInSeq(iseq1, seq1, l1, TRUE);
-		putBlobInSeq(iseq2, seq2, l2, FALSE);
+		putBlobInSeq(iseq1, seq1, l1, true);
+		putBlobInSeq(iseq2, seq2, l2, false);
 		// Compute alignment
 		id = sse_banded_lcs_align(iseq1, iseq2, l1, l2, normalize, reference, similarity_mode, address, LCSmin, lcs_length, ali_length);
 	}