Switch to version 3.0.0b43

not export the first line of data and switch to version 3.0.0b39

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,

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:])
@@ -263,8 +267,15 @@ 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(force=True)
     

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
@@ -15,7 +15,9 @@ from obitools3.libalign._solexapairend import buildConsensus, buildJoinedSequenc
 from obitools3.dms.obiseq cimport Nuc_Seq
 from obitools3.libalign.shifted_ali cimport Kmer_similarity, Ali_shifted
 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",
@@ -170,17 +174,28 @@ 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
@@ -206,18 +221,19 @@ 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:
@@ -226,31 +242,42 @@ def run(config):
                 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)
 
+    # 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(force=True)
-    output[0].close(force=True)
+    o_dms.close(force=True)
 
     logger("info", "Done.")
     

python/obitools3/commands/annotate.pyx

@@ -4,11 +4,12 @@ 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, \
@@ -34,6 +35,7 @@ def addOptions(parser):
     addMinimalInputOption(parser)
     addTaxonomyOption(parser)
     addMinimalOutputOption(parser)
+    addNoProgressBarOption(parser)
 
     group=parser.add_argument_group('obi annotate specific options')
  
@@ -278,8 +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:
@@ -307,7 +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:
 
@@ -346,14 +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:])
@@ -363,13 +381,19 @@ 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(force=True)
     i_dms.close(force=True)

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
 
@@ -88,14 +94,21 @@ def run(config):
     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(force=True)
     

python/obitools3/commands/cat.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 addMinimalOutputOption
+from obitools3.apps.optiongroups import addMinimalOutputOption, addNoProgressBarOption
 from obitools3.dms.view import RollbackException
 from obitools3.apps.config import logger
 from obitools3.utils cimport str2bytes
@@ -15,6 +15,7 @@ from obitools3.dms.capi.obiview cimport NUC_SEQUENCE_COLUMN, REVERSE_SEQUENCE_CO
 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
  
@@ -27,6 +28,7 @@ __title__="Concatenate views."
 def addOptions(parser):
     
     addMinimalOutputOption(parser)
+    addNoProgressBarOption(parser)
 
     group=parser.add_argument_group('obi cat specific options')
 
@@ -46,9 +48,9 @@ def run(config):
     
     logger("info", "obi cat")
 
-    # Open the views to concatenate
-    iview_list = []
+    # Check the views to concatenate
     idms_list = []
+    iview_list = []
     total_len = 0
     remove_qual = False
     remove_rev_qual = False
@@ -66,8 +68,9 @@ def run(config):
         if REVERSE_QUALITY_COLUMN not in i_view: # same as above for reverse quality
             remove_rev_qual = True
         total_len += len(i_view)
-        iview_list.append(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'],
@@ -76,57 +79,79 @@ 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]
     
+    # stdout output
+    if type(output_0)==BufferedWriter: 
+        o_dms = i_dms
+    
     # Initialize quality columns and their associated sequence columns if needed
-    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)
+    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
-    dict_cols = {}
-    for v in iview_list:
-        for coln in v.keys():
-            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'])
-    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']))
+    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']), dict_column=True)
     
     # Initialize the progress bar
-    pb = ProgressBar(total_len, config, seconde=5)
+    if not config['obi']['noprogressbar']:
+        pb = ProgressBar(total_len, config)
+    else:
+        pb = None
     
     i = 0
-    for v in iview_list:
-        for l in v:
+    for v_uri in config["cat"]["views_to_cat"]:
+        v = open_uri(v_uri)[1]
+        for entry in v:
             PyErr_CheckSignals()
-            pb(i)
-            o_view[i] = l
+            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 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 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)
     
-    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 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=[v.name for v in iview_list])
+    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)

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
 
 
@@ -21,6 +22,7 @@ def addOptions(parser):
 
     addMinimalInputOption(parser)
     addMinimalOutputOption(parser)
+    addNoProgressBarOption(parser)
     
     group = parser.add_argument_group('obi clean specific options')
 
@@ -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")
@@ -115,14 +122,21 @@ def run(config):
     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(force=True)
     

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",

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')
@@ -169,12 +171,21 @@ 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:])
     input_dms_name=[i_dms_name]
@@ -202,9 +213,20 @@ 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)
 
+    # 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)
 

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()
@@ -64,9 +77,8 @@ 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(ref_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'], ref_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'],
@@ -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
 
@@ -109,8 +123,9 @@ def run(config):
     if obi_ecotag(i_dms.name_with_full_path, tobytes(i_view_name), \
                   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']) < 0:
+                  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
@@ -120,11 +135,18 @@ 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(force=True)
     

python/obitools3/commands/export.pyx

@@ -74,7 +74,7 @@ def run(config):
     if config['obi']['noprogressbar']:
         pb = None
     else:
-        pb = ProgressBar(withoutskip - skip, config, seconde=5)
+        pb = ProgressBar(withoutskip - skip, config)
 
     i=0
     for seq in iview :
@@ -89,7 +89,7 @@ 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?
     

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")
  
@@ -182,7 +184,7 @@ def Filter_generator(options, tax_filter, i_view):
     invert_selection = options["invert_selection"]
     id_set = None
     if "id_list" in options:
-        id_set = set(x.strip() for x in open(options["id_list"]))
+        id_set = set(x.strip() for x in open(options["id_list"], 'rb'))
 
     # Initialize the regular expression patterns
     seq_pattern = None
@@ -304,16 +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
+    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 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))
+        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"])
@@ -324,7 +331,10 @@ 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"])
@@ -334,13 +344,15 @@ def run(config):
     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()
-            pb(i)
+            if pb is not None:
+                pb(i)
             selection.append(i)
     
     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()
-            pb(i)
+            if pb is not None:
+                pb(i)
             line = i_view[i]
             
             loc_env = {"sequence": line, "line": line, "taxonomy": taxo, "obi_eval_result": False}
@@ -350,8 +362,9 @@ def run(config):
             if good :
                 selection.append(i)
    
-    pb(len(i_view), force=True)
-    print("", file=sys.stderr)
+    if pb is not None:
+        pb(len(i_view), force=True)
+        print("", file=sys.stderr)
 
     # Create output view with the line selection
     try:
@@ -359,6 +372,8 @@ def run(config):
     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]
@@ -373,14 +388,20 @@ 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(force=True)
     i_dms.close(force=True)

python/obitools3/commands/head.pyx

@@ -4,13 +4,14 @@ 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))
+        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:
@@ -94,14 +106,20 @@ 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(force=True)
     i_dms.close(force=True)

python/obitools3/commands/import.pyx

@@ -26,13 +26,15 @@ from obitools3.dms.capi.obiview cimport VIEW_TYPE_NUC_SEQS, \
                                         QUALITY_COLUMN, \
                                         COUNT_COLUMN, \
                                         TAXID_COLUMN, \
-                                        MERGED_PREFIX
+                                        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
 
@@ -47,6 +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"
  
@@ -75,6 +79,11 @@ def addOptions(parser):
                      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):
     
@@ -87,6 +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
@@ -97,6 +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
@@ -130,7 +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:
@@ -140,7 +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
@@ -168,17 +180,20 @@ def run(config):
         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)
+        pb = ProgressBar(entry_count, config)
         
     NUC_SEQS_view = False
     if isinstance(output[1], View) :
@@ -194,6 +209,13 @@ def run(config):
         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
@@ -235,7 +257,8 @@ def run(config):
         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])), \
+                              elements_names=list(dict_dict[tag][0]), \
+                              dict_column=True), \
                           dict_dict[tag][1])
     
         
@@ -243,7 +266,7 @@ def run(config):
         if isinstance(input[0], CompressedFile):
             input_is_file = True
         if entry_count >= 0:
-            pb = ProgressBar(entry_count, config, seconde=5)
+            pb = ProgressBar(entry_count, config)
         try:
             input[0].close()
         except AttributeError:
@@ -284,6 +307,11 @@ def run(config):
                 if get_quality:
                     qual_col[i] = entry.quality
                     
+                # 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 
@@ -301,10 +329,13 @@ def run(config):
                         value_type = type(value)
                         nb_elts = 1
                         value_obitype = OBI_VOID
+                        dict_col = False
                          
                         if value_type == dict or value_type == list :
                             nb_elts = len(value)
                             elt_names = list(value)
+                            if value_type == dict :
+                                dict_col = True
                         else :
                             nb_elts = 1
                             elt_names = None
@@ -312,11 +343,9 @@ def run(config):
                         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)
+                            dcols[tag] = (Column.new_column(view, tag, value_obitype, nb_elements_per_line=nb_elts, elements_names=elt_names, dict_column=dict_col), 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?

python/obitools3/commands/ls.pyx

@@ -31,27 +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 viewname in input[0]:
-            view = dms[viewname]
-            l.append(tostr(viewname) + "\t(Date created: " + str(bytes2str_object(view.comments["Date created"]))+")")
-            view.close()
-        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
@@ -14,17 +14,14 @@ 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.dms.capi.obiview cimport REVERSE_SEQUENCE_COLUMN, REVERSE_QUALITY_COLUMN
-from obitools3.utils cimport tobytes
+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
-
-
-#REVERSE_SEQ_COLUMN_NAME = b"REVERSE_SEQUENCE"      # used by alignpairedend tool
-#REVERSE_QUALITY_COLUMN_NAME = b"REVERSE_QUALITY"   # used by alignpairedend tool
+from io import BufferedWriter
 
 
 __title__="Assigns sequence records to the corresponding experiment/sample based on DNA tags and primers"
@@ -34,6 +31,7 @@ def addOptions(parser):
 
     addMinimalInputOption(parser)
     addMinimalOutputOption(parser)
+    addNoProgressBarOption(parser)
     
     group = parser.add_argument_group('obi ngsfilter specific options')
 
@@ -58,7 +56,7 @@ 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",
@@ -539,6 +537,7 @@ 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"]:
         
@@ -580,8 +579,19 @@ 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:
@@ -602,7 +612,10 @@ 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
     try:
@@ -636,7 +649,8 @@ def run(config):
     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:
@@ -646,7 +660,13 @@ def run(config):
                 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:
         if unidentified is not None:
@@ -654,8 +674,9 @@ def run(config):
         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:])
@@ -664,13 +685,23 @@ def run(config):
         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)
+    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(force=True)
-    output[0].close(force=True)
+    # 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)

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')
 
@@ -86,19 +88,27 @@ 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))
+        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']
         
@@ -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'])
+        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'])
     
-    pb(len(i_view), force=True)
-    print("", file=sys.stderr)
+    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(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()

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))
+        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:])
@@ -97,14 +109,20 @@ 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(force=True)
     i_dms.close(force=True)

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
 
 
@@ -301,12 +302,16 @@ def create_random_column(config, infos) :
     alias = random.choice([b'', random_unique_name(infos)])
     tuples = random.choice([True, False])
     if not tuples :
+        dict_column = random.choice([True, False])
         nb_elements_per_line=random.randint(1, config['test']['maxelts'])
+        if nb_elements_per_line > 1:
+            dict_column = True
         elements_names = []
         for i in range(nb_elements_per_line) :
             elements_names.append(random_unique_element_name(config, infos))
         elements_names = random.choice([None, elements_names])
     else :
+        dict_column = False
         nb_elements_per_line = 1
         elements_names = None
     name = random_unique_name(infos)
@@ -317,6 +322,7 @@ def create_random_column(config, infos) :
                                data_type, 
                                nb_elements_per_line=nb_elements_per_line,
                                elements_names=elements_names,
+                               dict_column=dict_column,
                                tuples=tuples,
                                comments=random_comments(config),
                                alias=alias
@@ -366,7 +372,7 @@ 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 +447,7 @@ def addOptions(parser):
                        default=20,
                        type=int,
                        help="Maximum length of tuples. "
-                            "Default: 200")
+                            "Default: 20")
   
     group.add_argument('--max_ini_col_count','-o',
                        action="store", dest="test:maxinicolcount",
@@ -454,10 +460,10 @@ def addOptions(parser):
     group.add_argument('--max_line_nb','-l',
                        action="store", dest="test:maxlinenb",
                        metavar='<MAX_LINE_NB>',
-                       default=10000,
+                       default=1000,
                        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 +503,8 @@ 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 ???

python/obitools3/commands/uniq.pyx

@@ -14,13 +14,15 @@ 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"
@@ -32,6 +34,7 @@ def addOptions(parser):
     addTaxonomyOption(parser)
     addMinimalOutputOption(parser)
     addEltLimitOption(parser)
+    addNoProgressBarOption(parser)
  
     group = parser.add_argument_group('obi uniq specific options')
  
@@ -143,12 +146,16 @@ cdef merge_taxonomy_classification(View_NUC_SEQS o_view, Taxonomy taxonomy, dict
     scientific_name_column = o_view[b"scientific_name"]  
     
     # 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
     
     i=0
     for seq in o_view:
         PyErr_CheckSignals()
-        pb(i)
+        if pb is not None:
+            pb(i)
         if MERGED_TAXID_COLUMN in seq :
             m_taxids = []            
             m_taxids_dict = seq[MERGED_TAXID_COLUMN]
@@ -191,7 +198,8 @@ cdef merge_taxonomy_classification(View_NUC_SEQS o_view, Taxonomy taxonomy, dict
             scientific_name_column[i] = taxonomy.get_scientific_name(taxid)
         i+=1
     
-    pb(len(o_view), force=True)
+    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, dict config, list mergedKeys_list=None, Taxonomy taxonomy=None, bint mergeIds=False, list categories=None, int max_elts=1000000) :
@@ -297,7 +305,8 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, di
     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 
@@ -307,6 +316,7 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, di
         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
          
@@ -344,6 +354,9 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, di
         key = mergedKeys[k]
         merged_col_name = mergedKeys_m[k]
         
+        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:
@@ -365,6 +378,7 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, di
                               OBI_INT,
                               nb_elements_per_line=merged_infos[merged_col_name]['nb_elts'],
                               elements_names=list(merged_infos[merged_col_name]['elt_names']),
+                              dict_column=True,
                               comments=i_col.comments,
                               alias=merged_col_name
                              )
@@ -387,6 +401,7 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, di
                               OBI_INT,
                               nb_elements_per_line=len(view),
                               elements_names=[id for id in i_id_col],
+                              dict_column=True,
                               alias=TAXID_DIST_COLUMN
                              )
 
@@ -415,11 +430,16 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, di
     if COUNT_COLUMN in view:
         i_count_col = view[COUNT_COLUMN]
     
-    pb(len(view), force=True)
-    print("")
+    if pb is not None:
+        pb(len(view), force=True)
+        print("")
+        
     logger("info", "Second browsing through the input")
+    
     # Initialize the progress bar
-    pb = ProgressBar(len(view), seconde=5)
+    if pb is not None:
+        pb = ProgressBar(len(view))
+        
     o_idx = 0
     total_treated = 0
     
@@ -453,7 +473,10 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, di
             merged_dict[mkey] = {}
 
         for i_idx in merged_sequences:
-            pb(total_treated)
+            PyErr_CheckSignals()
+            
+            if pb is not None:
+                pb(total_treated)
  
             i_id = i_id_col[i_idx]
             i_seq = view[i_idx]
@@ -529,7 +552,8 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, di
         o_count_col[o_idx] = o_count
         o_idx += 1
     
-    pb(len(view), force=True)
+    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:
@@ -577,8 +601,23 @@ 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'])
@@ -589,7 +628,10 @@ 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
     
     if len(entries) > 0:
         try:
@@ -597,7 +639,8 @@ def run(config):
         except Exception, e:
             raise RollbackException("obi uniq error, rollbacking view: "+str(e), o_view)
     
-    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:])
@@ -607,13 +650,23 @@ 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(force=True)
-    output[0].close(force=True)
+    # 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

@@ -31,6 +31,7 @@ cdef extern from "obidmscolumn.h" nogil:
         const_char_p        elements_names
         OBIType_t           returned_data_type
         OBIType_t           stored_data_type
+        bint                dict_column
         bint                tuples
         bint                to_eval
         time_t              creation_date
@@ -63,10 +64,11 @@ cdef extern from "obidmscolumn.h" nogil:
     
     char* obi_get_elements_names(OBIDMS_column_p column)
     
-    char* obi_column_formatted_infos(OBIDMS_column_p column)
-
     index_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const char* element_name)
     
     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/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
@@ -52,6 +66,10 @@ cdef extern from "obidms_taxonomy.h" nogil:
     
     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)

python/obitools3/dms/capi/obiview.pxd

@@ -27,6 +27,7 @@ cdef extern from "obiview.h" nogil:
     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
@@ -94,6 +95,7 @@ cdef extern from "obiview.h" nogil:
                             index_t nb_elements_per_line,
                             char* elements_names,
                             bint  elt_names_formatted,
+                            bint dict_column,
                             bint tuples,
                             bint to_eval,
                             const_char_p indexer_name,
@@ -110,6 +112,10 @@ cdef extern from "obiview.h" nogil:
 
     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.pyx

@@ -40,6 +40,7 @@ from obitools3.utils cimport tobytes, \
 from obitools3.dms.column import typed_column
  
 from libc.stdlib cimport free
+from libc.string cimport strcpy
   
 import importlib
 import inspect
@@ -89,6 +90,7 @@ cdef class Column(OBIWrapper) :
                    obitype_t data_type,
                    index_t   nb_elements_per_line=1,
                    list      elements_names=None,
+                   bint      dict_column=False,
                    bint      tuples=False,
                    bint      to_eval=False,
                    object    associated_column_name=b"",
@@ -97,6 +99,7 @@ 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)))
@@ -140,6 +143,7 @@ cdef class Column(OBIWrapper) :
                     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,
                                 version_number            = -1,
@@ -149,6 +153,7 @@ cdef class Column(OBIWrapper) :
                                 nb_elements_per_line      = nb_elements_per_line,
                                 elements_names            = elements_names_p,
                                 elt_names_formatted       = False,
+                                dict_column               = dict_column,
                                 tuples                    = tuples,
                                 to_eval                   = to_eval,
                                 indexer_name              = NULL,
@@ -159,7 +164,18 @@ cdef class Column(OBIWrapper) :
             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
@@ -186,7 +202,7 @@ cdef class Column(OBIWrapper) :
         
         column_p = column_pp[0]
         column_type = column_p.header.returned_data_type
-        column_class = Column.get_column_class(column_type, (column_p.header.nb_elements_per_line > 1), column_p.header.tuples)
+        column_class = Column.get_column_class(column_type, (column_p.header.nb_elements_per_line > 1 or column_p.header.dict_column == True), column_p.header.tuples)
         column = OBIWrapper.new_wrapper(column_class, column_pp)
         
         column._view = view
@@ -222,6 +238,7 @@ cdef class Column(OBIWrapper) :
                                 nb_elements_per_line      = -1,
                                 elements_names            = NULL,
                                 elt_names_formatted       = False,
+                                dict_column               = False,
                                 tuples                    = False,
                                 to_eval                   = False,
                                 indexer_name              = NULL,
@@ -288,15 +305,24 @@ cdef class Column(OBIWrapper) :
     
     @OBIWrapper.checkIsActive
     def __repr__(self) :
-        cdef bytes s
-        #cdef char* s_b
-        #cdef str s_str
-        #s_b = obi_column_formatted_infos(self.pointer())
-        #s_str = bytes2str(s_b)
-        #free(s_b)
-        s = self._alias + b", data type: " + self.data_type
-        #return s_str
-        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
@@ -351,6 +377,13 @@ cdef class Column(OBIWrapper) :
             raise OBIDeactivatedInstanceError()
         return self.pointer().header.nb_elements_per_line
  
+    # dict_column property getter
+    @property
+    def dict_column(self):
+        if not self.active() :
+            raise OBIDeactivatedInstanceError()
+        return self.pointer().header.dict_column
+ 
     # data_type property getter
     @property
     def data_type(self):
@@ -407,6 +440,31 @@ 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/column/typed_column/bool.pyx

@@ -38,11 +38,13 @@ cdef class Column_bool(Column):
             object  column_name,
             index_t nb_elements_per_line=1,
             object  elements_names=None,
+            bint    dict_column=False,
             bint    tuples=False,
             object  comments={}):
         return Column.new_column(view, column_name, OBI_BOOL,
                           nb_elements_per_line=nb_elements_per_line, 
                           elements_names=elements_names,
+                          dict_column=dict_column, 
                           tuples=tuples,
                           comments=comments)
                 

python/obitools3/dms/column/typed_column/char.pyx

@@ -36,12 +36,14 @@ cdef class Column_char(Column):
             object  column_name,
             index_t nb_elements_per_line=1,
             object  elements_names=None,
+            bint    dict_column=False,
             bint    tuples=False,
             object  comments={}):
         
         return Column.new_column(view, column_name, OBI_CHAR,
                                  nb_elements_per_line=nb_elements_per_line, 
                                  elements_names=elements_names, 
+                                 dict_column=dict_column, 
                                  tuples=tuples,
                                  comments=comments)
 

python/obitools3/dms/column/typed_column/float.pyx

@@ -36,12 +36,14 @@ cdef class Column_float(Column):
             object  column_name,
             index_t nb_elements_per_line=1,
             object  elements_names=None,
+            bint    dict_column=False,
             bint    tuples=False,
             object  comments={}):
         
         return Column.new_column(view, column_name, OBI_FLOAT,
                                  nb_elements_per_line=nb_elements_per_line, 
                                  elements_names=elements_names, 
+                                 dict_column=dict_column, 
                                  tuples=tuples,
                                  comments=comments)
 

python/obitools3/dms/column/typed_column/int.pyx

@@ -38,12 +38,14 @@ cdef class Column_int(Column):
             object  column_name,
             index_t nb_elements_per_line=1,
             object  elements_names=None,
+            bint    dict_column=False,
             bint    tuples=False,
             object  comments={}):
         
         return Column.new_column(view, column_name, OBI_INT,
                                  nb_elements_per_line=nb_elements_per_line, 
                                  elements_names=elements_names, 
+                                 dict_column=dict_column, 
                                  tuples=tuples,
                                  comments=comments)
 

python/obitools3/dms/column/typed_column/qual.pyx

@@ -38,6 +38,7 @@ cdef class Column_qual(Column_idx):
             object  column_name,
             index_t nb_elements_per_line=1,
             object  elements_names=None,
+            bint    dict_column=False,
             object  associated_column_name=b"",
             int     associated_column_version=-1,
             object  comments={}):
@@ -45,6 +46,7 @@ cdef class Column_qual(Column_idx):
         return Column.new_column(view, column_name, OBI_QUAL,
                                  nb_elements_per_line=nb_elements_per_line, 
                                  elements_names=elements_names, 
+                                 dict_column=dict_column, 
                                  tuples=False,
                                  associated_column_name=associated_column_name,
                                  associated_column_version=associated_column_name,

python/obitools3/dms/column/typed_column/seq.pyx

@@ -39,12 +39,14 @@ cdef class Column_seq(Column_idx):
             object  column_name,
             index_t nb_elements_per_line=1,
             object  elements_names=None,
+            bint    dict_column=False,
             bint    tuples=False,
             object  comments={}):
         
         return Column.new_column(view, column_name, OBI_SEQ,
                                  nb_elements_per_line=nb_elements_per_line, 
                                  elements_names=elements_names, 
+                                 dict_column=dict_column, 
                                  tuples=tuples,
                                  comments=comments)
 

python/obitools3/dms/column/typed_column/str.pyx

@@ -38,12 +38,14 @@ cdef class Column_str(Column_idx):
             object  column_name,
             index_t nb_elements_per_line=1,
             object  elements_names=None,
+            bint    dict_column=False,
             bint    tuples=False,
             object  comments={}):
         
         return Column.new_column(view, column_name, OBI_STR,
                                  nb_elements_per_line=nb_elements_per_line, 
                                  elements_names=elements_names, 
+                                 dict_column=dict_column, 
                                  tuples=tuples,
                                  comments=comments)
 

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):    
     
@@ -223,13 +226,24 @@ cdef class DMS(OBIWrapper):
 
 
     @OBIWrapper.checkIsActive
-    def __repr__(self):
+    def __repr__(self) :
         cdef str s
-        s=""
-        for view_name in self.keys():
-            view = self.get_view(view_name)
-            s = s + repr(view) + "\n"
-            view.close()
+        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
     
 

python/obitools3/dms/obiseq.pxd

@@ -40,3 +40,5 @@ cdef class Nuc_Seq_Stored(Seq_Stored) :
     cpdef object build_quality_array(self, list quality)
     cpdef bytes build_reverse_complement(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
@@ -29,6 +33,24 @@ cdef class Taxonomy(OBIWrapper) :
     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

@@ -21,6 +21,10 @@ cdef class View(OBIWrapper):
     
     cdef inline Obiview_p pointer(self)   
 
+    cpdef print_to_output(self, 
+                          object output, 
+                          bint noprogressbar=*)
+        
     cpdef delete_column(self, 
                         object column_name,
                         bint delete_file=*)
@@ -61,6 +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) :
@@ -179,13 +189,50 @@ 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'
+        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):
         
         cdef bytes               col_alias
@@ -296,7 +343,7 @@ cdef class View(OBIWrapper) :
 
         new_column = Column.new_column(self, old_column.pointer().header.name, new_data_type, 
                                        nb_elements_per_line=new_nb_elements_per_line, elements_names=new_elements_names, 
-                                       comments=old_column.comments, alias=column_name_b+tobytes('___new___'))
+                                       dict_column=(new_nb_elements_per_line>1), 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]
@@ -357,6 +404,7 @@ cdef class View(OBIWrapper) :
                                   col.data_type_int, 
                                   nb_elements_per_line = col.nb_elements_per_line,
                                   elements_names = col._elements_names,
+                                  dict_column = col.dict_column,
                                   tuples = col.tuples,
                                   to_eval = col.to_eval,
                                   comments = col.comments,
@@ -405,6 +453,7 @@ 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)
 
     
@@ -757,8 +806,12 @@ 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

@@ -5,6 +5,7 @@ from obitools3.dms.view.view cimport Line
 from obitools3.utils cimport bytes2str_object, str2bytes, tobytes
 from obitools3.dms.column.column cimport Column_line, Column_multi_elts
 
+import sys
 
 cdef class TabFormat:
     
@@ -22,33 +23,45 @@ cdef class TabFormat:
         if self.first_line:
             self.tags = [k for k in data.keys()]
         
-        for k in self.tags:
-            
-            if self.header and self.first_line:
+        if self.header and self.first_line:
+            for k in self.tags:
                 if isinstance(data.view[k], Column_multi_elts):
-                    for k2 in data.view[k].keys():
+                    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 isinstance(data.view[k], Column_multi_elts):
-                    if value is None:  # all keys at None
-                        for k2 in data.view[k].keys(): # TODO could be much more efficient
-                            line.append(self.NAString)
-                    else:
-                        for k2 in data.view[k].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:
+            r = self.sep.join(value for value in line)
+            r += b'\n'
+            line = []
+                    
+        for k in self.tags:
+            value = data[k]
+            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:
+                    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.header and self.first_line:
+            r += self.sep.join(value for value in line)
+        else:
+            r = self.sep.join(value for value in line)
 
         if self.first_line:
             self.first_line = False
 
-        return self.sep.join(value for value in line)
+        return r

python/obitools3/libalign/_solexapairend.pyx

@@ -183,8 +183,9 @@ 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?
@@ -256,9 +257,10 @@ def buildJoinedSequence(ali, reverse, seq, forward=None):
         seq[b"ali_direction"]=None
     seq[b"mode"]=b"joined"
     seq[b"pairedend_limit"]=len(forward)
-    seq[b"ali_length"] = ali.consensus_len
-    if ali.consensus_len > 0:
-        seq[b"score_norm"]=float(ali.score)/ali.consensus_len
+    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
   

python/obitools3/parsers/genbank.pyx

@@ -22,10 +22,10 @@ from libc.stdlib  cimport free, malloc, realloc
 from libc.string cimport strcpy, strlen
 
 
-_featureMatcher = re.compile(b'^FEATURES.+\n(?=ORIGIN)',re.DOTALL + re.M)
+_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)
+_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)

python/obitools3/uri/decode.pyx

@@ -210,10 +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)
@@ -275,10 +276,10 @@ 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)
@@ -463,7 +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" and format != b"embl" and format != b"genbank":
+            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:

python/obitools3/version.py

@@ -1,5 +1,5 @@
 major = 3
 minor = 0
-serial= '0b26'
+serial= '0b43'
 
 version ="%d.%d.%s" % (major,minor,serial)

src/build_reference_db.c

@@ -243,6 +243,7 @@ int build_reference_db(const char* dms_name,
 							false,
 							false,
 							false,
+							false,
 							"",
 							"",
 							-1,
@@ -392,6 +393,7 @@ int build_reference_db(const char* dms_name,
 							1,
 							"",
 							false,
+							false,
 							true,
 							false,
 							"",
@@ -415,6 +417,7 @@ int build_reference_db(const char* dms_name,
 							1,
 							"",
 							false,
+							false,
 							true,
 							false,
 							"",

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

@@ -414,7 +414,10 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
 	}
 
 	if (max_common_kmers > 0)
-		score = max_common_kmers + kmer_size - 1;  // aka the number of nucleotides in the longest stretch of kmers perfectly matching
+		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);

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

@@ -88,42 +88,42 @@ static int create_output_columns(Obiview_p o_view,
 								 int sample_count)
 {
 	// Status column
-	if (obi_view_add_column(o_view, CLEAN_STATUS_COLUMN_NAME, -1, NULL, OBI_CHAR, 0, sample_count, (sample_column->header)->elements_names, true, false, false, NULL, NULL, -1, CLEAN_STATUS_COLUMN_COMMENTS, true) < 0)
+	if (obi_view_add_column(o_view, CLEAN_STATUS_COLUMN_NAME, -1, NULL, OBI_CHAR, 0, sample_count, (sample_column->header)->elements_names, true, true, false, false, NULL, NULL, -1, CLEAN_STATUS_COLUMN_COMMENTS, true) < 0)
 	{
 		obidebug(1, "\nError creating the %s column", CLEAN_STATUS_COLUMN_NAME);
 		return -1;
 	}
 
 	// Head column
-	if (obi_view_add_column(o_view, CLEAN_HEAD_COLUMN_NAME, -1, NULL, OBI_BOOL, 0, 1, NULL, false, false, false, NULL, NULL, -1, CLEAN_HEAD_COLUMN_COMMENTS, true) < 0)
+	if (obi_view_add_column(o_view, CLEAN_HEAD_COLUMN_NAME, -1, NULL, OBI_BOOL, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, CLEAN_HEAD_COLUMN_COMMENTS, true) < 0)
 	{
 		obidebug(1, "\nError creating the %s column", CLEAN_HEAD_COLUMN_NAME);
 		return -1;
 	}
 
 	// Sample count column
-	if (obi_view_add_column(o_view, CLEAN_SAMPLECOUNT_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, CLEAN_SAMPLECOUNT_COLUMN_COMMENTS, true) < 0)
+	if (obi_view_add_column(o_view, CLEAN_SAMPLECOUNT_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, CLEAN_SAMPLECOUNT_COLUMN_COMMENTS, true) < 0)
 	{
 		obidebug(1, "\nError creating the %s column", CLEAN_SAMPLECOUNT_COLUMN_NAME);
 		return -1;
 	}
 
 	// Head count column
-	if (obi_view_add_column(o_view, CLEAN_HEADCOUNT_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, CLEAN_HEADCOUNT_COLUMN_COMMENTS, true) < 0)
+	if (obi_view_add_column(o_view, CLEAN_HEADCOUNT_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, CLEAN_HEADCOUNT_COLUMN_COMMENTS, true) < 0)
 	{
 		obidebug(1, "\nError creating the %s column", CLEAN_HEADCOUNT_COLUMN_NAME);
 		return -1;
 	}
 
 	// Internal count column
-	if (obi_view_add_column(o_view, CLEAN_INTERNALCOUNT_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, CLEAN_INTERNALCOUNT_COLUMN_COMMENTS, true) < 0)
+	if (obi_view_add_column(o_view, CLEAN_INTERNALCOUNT_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, CLEAN_INTERNALCOUNT_COLUMN_COMMENTS, true) < 0)
 	{
 		obidebug(1, "\nError creating the %s column", CLEAN_INTERNALCOUNT_COLUMN_NAME);
 		return -1;
 	}
 
 	// Singleton count column
-	if (obi_view_add_column(o_view, CLEAN_SINGLETONCOUNT_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, CLEAN_SINGLETONCOUNT_COLUMN_COMMENTS, true) < 0)
+	if (obi_view_add_column(o_view, CLEAN_SINGLETONCOUNT_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, CLEAN_SINGLETONCOUNT_COLUMN_COMMENTS, true) < 0)
 	{
 		obidebug(1, "\nError creating the %s column", CLEAN_SINGLETONCOUNT_COLUMN_NAME);
 		return -1;
@@ -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)
 	{
@@ -549,7 +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

@@ -150,49 +150,49 @@ static int print_seq(Obiview_p i_view, Obiview_p o_view,
 static int create_output_columns(Obiview_p o_view, bool kingdom_mode)
 {
 	// Original length column
-	if (obi_view_add_column(o_view, ECOPCR_SEQLEN_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_SEQLEN_COLUMN_COMMENTS, true) < 0)
+	if (obi_view_add_column(o_view, ECOPCR_SEQLEN_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_SEQLEN_COLUMN_COMMENTS, true) < 0)
 	{
 		obidebug(1, "\nError creating the %s column", ECOPCR_SEQLEN_COLUMN_NAME);
 		return -1;
 	}
 
 	// Amplicon length column
-	if (obi_view_add_column(o_view, ECOPCR_AMPLICONLEN_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_AMPLICONLEN_COLUMN_COMMENTS, true) < 0)
+	if (obi_view_add_column(o_view, ECOPCR_AMPLICONLEN_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_AMPLICONLEN_COLUMN_COMMENTS, true) < 0)
 	{
 		obidebug(1, "\nError creating the %s column", ECOPCR_AMPLICONLEN_COLUMN_NAME);
 		return -1;
 	}
 
 	// Taxid column
-	if (obi_view_add_column(o_view, TAXID_COLUMN, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, TAXID_COLUMN_COMMENTS, true) < 0)
+	if (obi_view_add_column(o_view, TAXID_COLUMN, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, TAXID_COLUMN_COMMENTS, true) < 0)
 	{
 		obidebug(1, "\nError creating the %s column", TAXID_COLUMN);
 		return -1;
 	}
 
 	// Taxonomic rank column
-	if (obi_view_add_column(o_view, ECOPCR_RANK_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_RANK_COLUMN_COMMENTS, true) < 0)
+	if (obi_view_add_column(o_view, ECOPCR_RANK_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_RANK_COLUMN_COMMENTS, true) < 0)
 	{
 		obidebug(1, "\nError creating the %s column", ECOPCR_RANK_COLUMN_NAME);
 		return -1;
 	}
 
 	// Species taxid column
-	if (obi_view_add_column(o_view, ECOPCR_SPECIES_TAXID_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_SPECIES_TAXID_COLUMN_COMMENTS, true) < 0)
+	if (obi_view_add_column(o_view, ECOPCR_SPECIES_TAXID_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_SPECIES_TAXID_COLUMN_COMMENTS, true) < 0)
 	{
 		obidebug(1, "\nError creating the %s column", ECOPCR_SPECIES_TAXID_COLUMN_NAME);
 		return -1;
 	}
 
 	// Genus taxid column
-	if (obi_view_add_column(o_view, ECOPCR_GENUS_TAXID_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_GENUS_TAXID_COLUMN_COMMENTS, true) < 0)
+	if (obi_view_add_column(o_view, ECOPCR_GENUS_TAXID_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_GENUS_TAXID_COLUMN_COMMENTS, true) < 0)
 	{
 		obidebug(1, "\nError creating the %s column", ECOPCR_GENUS_TAXID_COLUMN_NAME);
 		return -1;
 	}
 
 	// Family taxid column
-	if (obi_view_add_column(o_view, ECOPCR_FAMILY_TAXID_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_FAMILY_TAXID_COLUMN_COMMENTS, true) < 0)
+	if (obi_view_add_column(o_view, ECOPCR_FAMILY_TAXID_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_FAMILY_TAXID_COLUMN_COMMENTS, true) < 0)
 	{
 		obidebug(1, "\nError creating the %s column", ECOPCR_FAMILY_TAXID_COLUMN_NAME);
 		return -1;
@@ -201,7 +201,7 @@ static int create_output_columns(Obiview_p o_view, bool kingdom_mode)
 	if (kingdom_mode)
 	{
 		// Kingdom taxid column
-		if (obi_view_add_column(o_view, ECOPCR_KINGDOM_TAXID_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_KINGDOM_TAXID_COLUMN_COMMENTS, true) < 0)
+		if (obi_view_add_column(o_view, ECOPCR_KINGDOM_TAXID_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_KINGDOM_TAXID_COLUMN_COMMENTS, true) < 0)
 		{
 			obidebug(1, "\nError creating the %s column", ECOPCR_KINGDOM_TAXID_COLUMN_NAME);
 			return -1;
@@ -210,7 +210,7 @@ static int create_output_columns(Obiview_p o_view, bool kingdom_mode)
 	else
 	{
 		// Superkingdom taxid column
-		if (obi_view_add_column(o_view, ECOPCR_SUPERKINGDOM_TAXID_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_SUPERKINGDOM_TAXID_COLUMN_COMMENTS, true) < 0)
+		if (obi_view_add_column(o_view, ECOPCR_SUPERKINGDOM_TAXID_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_SUPERKINGDOM_TAXID_COLUMN_COMMENTS, true) < 0)
 		{
 			obidebug(1, "\nError creating the %s column", ECOPCR_SUPERKINGDOM_TAXID_COLUMN_NAME);
 			return -1;
@@ -218,28 +218,28 @@ static int create_output_columns(Obiview_p o_view, bool kingdom_mode)
 	}
 
 	// Scientific name column
-	if (obi_view_add_column(o_view, ECOPCR_SCIENTIFIC_NAME_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_SCIENTIFIC_NAME_COLUMN_COMMENTS, true) < 0)
+	if (obi_view_add_column(o_view, ECOPCR_SCIENTIFIC_NAME_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_SCIENTIFIC_NAME_COLUMN_COMMENTS, true) < 0)
 	{
 		obidebug(1, "\nError creating the %s column", ECOPCR_SCIENTIFIC_NAME_COLUMN_NAME);
 		return -1;
 	}
 
 	// Species name column
-	if (obi_view_add_column(o_view, ECOPCR_SPECIES_NAME_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_SPECIES_NAME_COLUMN_COMMENTS, true) < 0)
+	if (obi_view_add_column(o_view, ECOPCR_SPECIES_NAME_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_SPECIES_NAME_COLUMN_COMMENTS, true) < 0)
 	{
 		obidebug(1, "\nError creating the %s column", ECOPCR_SPECIES_NAME_COLUMN_NAME);
 		return -1;
 	}
 
 	// Genus name column
-	if (obi_view_add_column(o_view, ECOPCR_GENUS_NAME_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_GENUS_NAME_COLUMN_COMMENTS, true) < 0)
+	if (obi_view_add_column(o_view, ECOPCR_GENUS_NAME_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_GENUS_NAME_COLUMN_COMMENTS, true) < 0)
 	{
 		obidebug(1, "\nError creating the %s column", ECOPCR_GENUS_NAME_COLUMN_NAME);
 		return -1;
 	}
 
 	// Family name column
-	if (obi_view_add_column(o_view, ECOPCR_FAMILY_NAME_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_FAMILY_NAME_COLUMN_COMMENTS, true) < 0)
+	if (obi_view_add_column(o_view, ECOPCR_FAMILY_NAME_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_FAMILY_NAME_COLUMN_COMMENTS, true) < 0)
 	{
 		obidebug(1, "\nError creating the %s column", ECOPCR_FAMILY_NAME_COLUMN_NAME);
 		return -1;
@@ -248,7 +248,7 @@ static int create_output_columns(Obiview_p o_view, bool kingdom_mode)
 	if (kingdom_mode)
 	{
 		// Kingdom name column
-		if (obi_view_add_column(o_view, ECOPCR_KINGDOM_NAME_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_KINGDOM_NAME_COLUMN_COMMENTS, true) < 0)
+		if (obi_view_add_column(o_view, ECOPCR_KINGDOM_NAME_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_KINGDOM_NAME_COLUMN_COMMENTS, true) < 0)
 		{
 			obidebug(1, "\nError creating the %s column", ECOPCR_KINGDOM_NAME_COLUMN_NAME);
 			return -1;
@@ -257,7 +257,7 @@ static int create_output_columns(Obiview_p o_view, bool kingdom_mode)
 	else
 	{
 		// Superkingdom name column
-		if (obi_view_add_column(o_view, ECOPCR_SUPERKINGDOM_NAME_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_SUPERKINGDOM_NAME_COLUMN_COMMENTS, true) < 0)
+		if (obi_view_add_column(o_view, ECOPCR_SUPERKINGDOM_NAME_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_SUPERKINGDOM_NAME_COLUMN_COMMENTS, true) < 0)
 		{
 			obidebug(1, "\nError creating the %s column", ECOPCR_SUPERKINGDOM_NAME_COLUMN_NAME);
 			return -1;
@@ -265,49 +265,49 @@ static int create_output_columns(Obiview_p o_view, bool kingdom_mode)
 	}
 
 	// Strand column
-	if (obi_view_add_column(o_view, ECOPCR_STRAND_COLUMN_NAME, -1, NULL, OBI_CHAR, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_STRAND_COLUMN_COMMENTS, true) < 0)
+	if (obi_view_add_column(o_view, ECOPCR_STRAND_COLUMN_NAME, -1, NULL, OBI_CHAR, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_STRAND_COLUMN_COMMENTS, true) < 0)
 	{
 		obidebug(1, "\nError creating the %s column", ECOPCR_STRAND_COLUMN_NAME);
 		return -1;
 	}
 
 	// Primer 1 column
-	if (obi_view_add_column(o_view, ECOPCR_PRIMER1_COLUMN_NAME, -1, NULL, OBI_SEQ, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_PRIMER1_COLUMN_COMMENTS, true) < 0)
+	if (obi_view_add_column(o_view, ECOPCR_PRIMER1_COLUMN_NAME, -1, NULL, OBI_SEQ, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_PRIMER1_COLUMN_COMMENTS, true) < 0)
 	{
 		obidebug(1, "\nError creating the %s column", ECOPCR_PRIMER1_COLUMN_NAME);
 		return -1;
 	}
 
 	// Primer 2 column
-	if (obi_view_add_column(o_view, ECOPCR_PRIMER2_COLUMN_NAME, -1, NULL, OBI_SEQ, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_PRIMER2_COLUMN_COMMENTS, true) < 0)
+	if (obi_view_add_column(o_view, ECOPCR_PRIMER2_COLUMN_NAME, -1, NULL, OBI_SEQ, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_PRIMER2_COLUMN_COMMENTS, true) < 0)
 	{
 		obidebug(1, "\nError creating the %s column", ECOPCR_PRIMER2_COLUMN_NAME);
 		return -1;
 	}
 
 	// Error 1 column
-	if (obi_view_add_column(o_view, ECOPCR_ERROR1_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_ERROR1_COLUMN_COMMENTS, true) < 0)
+	if (obi_view_add_column(o_view, ECOPCR_ERROR1_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_ERROR1_COLUMN_COMMENTS, true) < 0)
 	{
 		obidebug(1, "\nError creating the %s column", ECOPCR_ERROR1_COLUMN_NAME);
 		return -1;
 	}
 
 	// Error 2 column
-	if (obi_view_add_column(o_view, ECOPCR_ERROR2_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_ERROR2_COLUMN_COMMENTS, true) < 0)
+	if (obi_view_add_column(o_view, ECOPCR_ERROR2_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_ERROR2_COLUMN_COMMENTS, true) < 0)
 	{
 		obidebug(1, "\nError creating the %s column", ECOPCR_ERROR2_COLUMN_NAME);
 		return -1;
 	}
 
 	// Temperature 1 column
-	if (obi_view_add_column(o_view, ECOPCR_TEMP1_COLUMN_NAME, -1, NULL, OBI_FLOAT, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_TEMP1_COLUMN_COMMENTS, true) < 0)
+	if (obi_view_add_column(o_view, ECOPCR_TEMP1_COLUMN_NAME, -1, NULL, OBI_FLOAT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_TEMP1_COLUMN_COMMENTS, true) < 0)
 	{
 		obidebug(1, "\nError creating the %s column", ECOPCR_TEMP1_COLUMN_NAME);
 		return -1;
 	}
 
 	// Temperature 2 column
-	if (obi_view_add_column(o_view, ECOPCR_TEMP2_COLUMN_NAME, -1, NULL, OBI_FLOAT, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_TEMP2_COLUMN_COMMENTS, true) < 0)
+	if (obi_view_add_column(o_view, ECOPCR_TEMP2_COLUMN_NAME, -1, NULL, OBI_FLOAT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_TEMP2_COLUMN_COMMENTS, true) < 0)
 	{
 		obidebug(1, "\nError creating the %s column", ECOPCR_TEMP2_COLUMN_NAME);
 		return -1;

src/obi_ecotag.c

@@ -104,42 +104,42 @@ 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, "{}", true) < 0)
+	if (obi_view_add_column(o_view, ECOTAG_SCORE_COLUMN_NAME, -1, NULL, OBI_FLOAT, 0, 1, NULL, false, 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, "{}", true) < 0)
+	if (obi_view_add_column(o_view, ECOTAG_TAXID_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, 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, "{}", true) < 0)
+	if (obi_view_add_column(o_view, ECOTAG_NAME_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, 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, "{}", true) < 0)
+	if (obi_view_add_column(o_view, ECOTAG_STATUS_COLUMN_NAME, -1, NULL, OBI_BOOL, 0, 1, NULL, false, 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, "{}", true) < 0)
+	if (obi_view_add_column(o_view, ECOTAG_BEST_MATCH_IDS_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, true, false, NULL, NULL, -1, "{}", true) < 0)
 	{
 		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)
+	if (obi_view_add_column(o_view, ECOTAG_BEST_MATCH_TAXIDS_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, 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;
@@ -218,7 +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
@@ -239,6 +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;
@@ -389,10 +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;
 	}
 
@@ -597,11 +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] >= best_score))
+			while ((k < lca_array_length) && (score_array[k] >= lca_threshold))
 				k++;
 
 			if (k>0)

src/obi_ecotag.h

@@ -42,12 +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.
@@ -65,7 +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/obi_lcs.c

@@ -155,35 +155,35 @@ static int create_alignment_output_columns(Obiview_p output_view,
 										   bool normalize, int reference, bool similarity_mode)
 {
 	// Create the column for the ids of the 1st sequence aligned
-	if (obi_view_add_column(output_view, ID1_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, id1_indexer_name, NULL, -1, ID1_COLUMN_COMMENTS, true) < 0)
+	if (obi_view_add_column(output_view, ID1_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, false, id1_indexer_name, NULL, -1, ID1_COLUMN_COMMENTS, true) < 0)
 	{
 		obidebug(1, "\nError creating the first column for the sequence ids when aligning");
 		return -1;
 	}
 
 	// Create the column for the ids of the 2nd sequence aligned
-	if (obi_view_add_column(output_view, ID2_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, id2_indexer_name, NULL, -1, ID2_COLUMN_COMMENTS, true) < 0)
+	if (obi_view_add_column(output_view, ID2_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, false, id2_indexer_name, NULL, -1, ID2_COLUMN_COMMENTS, true) < 0)
 	{
 		obidebug(1, "\nError creating the second column for the sequence ids when aligning");
 		return -1;
 	}
 
 	// Create the column for the index (in the input view) of the first sequences aligned
-	if (obi_view_add_column(output_view, IDX1_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, IDX1_COLUMN_COMMENTS, true) < 0)
+	if (obi_view_add_column(output_view, IDX1_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, IDX1_COLUMN_COMMENTS, true) < 0)
 	{
 		obidebug(1, "\nError creating the first column for the sequence indices when aligning");
 		return -1;
 	}
 
 	// Create the column for the index (in the input view) of the second sequences aligned
-	if (obi_view_add_column(output_view, IDX2_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, IDX2_COLUMN_COMMENTS, true) < 0)
+	if (obi_view_add_column(output_view, IDX2_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, IDX2_COLUMN_COMMENTS, true) < 0)
 	{
 		obidebug(1, "\nError creating the second column for the sequence indices when aligning");
 		return -1;
 	}
 
 	// Create the column for the LCS length
-	if (obi_view_add_column(output_view, LCS_LENGTH_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, LCS_LENGTH_COLUMN_COMMENTS, true) < 0)
+	if (obi_view_add_column(output_view, LCS_LENGTH_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, LCS_LENGTH_COLUMN_COMMENTS, true) < 0)
 	{
 		obidebug(1, "\nError creating the column for the LCS length when aligning");
 		return -1;
@@ -192,7 +192,7 @@ static int create_alignment_output_columns(Obiview_p output_view,
 	// Create the column for the alignment length if it is computed
 	if ((reference == ALILEN) && (normalize || !similarity_mode))
 	{
-		if (obi_view_add_column(output_view, ALI_LENGTH_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, ALI_LENGTH_COLUMN_COMMENTS, true) < 0)
+		if (obi_view_add_column(output_view, ALI_LENGTH_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ALI_LENGTH_COLUMN_COMMENTS, true) < 0)
 		{
 			obidebug(1, "\nError creating the column for the alignment length when aligning");
 			return -1;
@@ -201,7 +201,7 @@ static int create_alignment_output_columns(Obiview_p output_view,
 	// Create the column for the alignment score
 	if (normalize)
 	{
-		if (obi_view_add_column(output_view, SCORE_COLUMN_NAME, -1, NULL, OBI_FLOAT, 0, 1, NULL, false, false, false, NULL, NULL, -1, SCORE_COLUMN_NAME, true) < 0)
+		if (obi_view_add_column(output_view, SCORE_COLUMN_NAME, -1, NULL, OBI_FLOAT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, SCORE_COLUMN_NAME, true) < 0)
 		{
 			obidebug(1, "\nError creating the column for the score when aligning");
 			return -1;
@@ -209,7 +209,7 @@ static int create_alignment_output_columns(Obiview_p output_view,
 	}
 	else
 	{
-		if (obi_view_add_column(output_view, SCORE_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, SCORE_COLUMN_NAME, true) < 0)
+		if (obi_view_add_column(output_view, SCORE_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, SCORE_COLUMN_NAME, true) < 0)
 		{
 			obidebug(1, "\nError creating the column for the score when aligning");
 			return -1;
@@ -219,14 +219,14 @@ static int create_alignment_output_columns(Obiview_p output_view,
 	if (print_seq)
 	{
 		// Create the column for the first sequences aligned
-		if (obi_view_add_column(output_view, SEQ1_COLUMN_NAME, -1, NULL, OBI_SEQ, 0, 1, NULL, false, false, false, seq1_indexer_name, NULL, -1, SEQ1_COLUMN_COMMENTS, true) < 0)
+		if (obi_view_add_column(output_view, SEQ1_COLUMN_NAME, -1, NULL, OBI_SEQ, 0, 1, NULL, false, false, false, false, seq1_indexer_name, NULL, -1, SEQ1_COLUMN_COMMENTS, true) < 0)
 		{
 			obidebug(1, "\nError creating the first column for the sequences when aligning");
 			return -1;
 		}
 
 		// Create the column for the second sequences aligned
-		if (obi_view_add_column(output_view, SEQ2_COLUMN_NAME, -1, NULL, OBI_SEQ, 0, 1, NULL, false, false, false, seq2_indexer_name, NULL, -1, SEQ2_COLUMN_COMMENTS, true) < 0)
+		if (obi_view_add_column(output_view, SEQ2_COLUMN_NAME, -1, NULL, OBI_SEQ, 0, 1, NULL, false, false, false, false, seq2_indexer_name, NULL, -1, SEQ2_COLUMN_COMMENTS, true) < 0)
 		{
 			obidebug(1, "\nError creating the second column for the sequences when aligning");
 			return -1;
@@ -235,14 +235,14 @@ static int create_alignment_output_columns(Obiview_p output_view,
 	if (print_count)
 	{
 		// Create the column for the count of the first sequences aligned
-		if (obi_view_add_column(output_view, COUNT1_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, COUNT1_COLUMN_COMMENTS, true) < 0)
+		if (obi_view_add_column(output_view, COUNT1_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, COUNT1_COLUMN_COMMENTS, true) < 0)
 		{
 			obidebug(1, "\nError creating the first column for the sequence counts when aligning");
 			return -1;
 		}
 
 		// Create the column for the count of the second sequences aligned
-		if (obi_view_add_column(output_view, COUNT2_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, COUNT2_COLUMN_COMMENTS, true) < 0)
+		if (obi_view_add_column(output_view, COUNT2_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, COUNT2_COLUMN_COMMENTS, true) < 0)
 		{
 			obidebug(1, "\nError creating the second column for the sequence counts when aligning");
 			return -1;

src/obiavl.c

@@ -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

@@ -1409,6 +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)
@@ -1474,8 +1575,8 @@ obiversion_t obi_import_column(const char* dms_path_1, const char* dms_path_2, c
 
 	// Create new column
 	column_2 = obi_create_column(dms_2, column_name, header_1->returned_data_type, header_1->line_count,
-								 header_1->nb_elements_per_line, header_1->elements_names, true, header_1->tuples,
-								 header_1->to_eval, new_avl_name, (header_1->associated_column).column_name,
+								 header_1->nb_elements_per_line, header_1->elements_names, true, header_1->dict_column,
+								 header_1->tuples, header_1->to_eval, new_avl_name, (header_1->associated_column).column_name,
 								 (header_1->associated_column).version, header_1->comments);
 
 	if (column_2 == NULL)
@@ -1659,6 +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;
 
@@ -1706,6 +1813,7 @@ int obi_import_view(const char* dms_path_1, const char* dms_path_2, const char*
 								false,
 								false,
 								false,
+								false,
 								NULL,
 								NULL,
 								-1,

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

@@ -3649,6 +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

@@ -1024,6 +1024,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p     dms,
 								  index_t      nb_elements_per_line,
 								  char*        elements_names,
 								  bool		   elt_names_formatted,
+								  bool         dict_column,
 								  bool		   tuples,
 								  bool         to_eval,
 								  const char*  indexer_name,
@@ -1282,6 +1283,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p     dms,
 	header->nb_elements_per_line          = nb_elements_per_line;
 	header->stored_data_type     		  = stored_data_type;
 	header->returned_data_type   		  = returned_data_type;
+	header->dict_column     			  = dict_column;
 	header->tuples     					  = tuples;
 	header->to_eval                       = to_eval;
 	header->creation_date 		 		  = time(NULL);
@@ -1312,19 +1314,10 @@ 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 +1329,7 @@ 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)
 	{
@@ -1619,6 +1613,7 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p         dms,
 								   nb_elements_per_line,
 								   (column_to_clone->header)->elements_names,
 								   true,
+								   (column_to_clone->header)->dict_column,
 								   (column_to_clone->header)->tuples,
 								   (column_to_clone->header)->to_eval,
 								   (column_to_clone->header)->indexer_name,
@@ -1733,16 +1728,32 @@ 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);
@@ -2423,17 +2434,81 @@ char* obi_get_formatted_elements_names(OBIDMS_column_p column)
 }
 
 
-char* obi_column_formatted_infos(OBIDMS_column_p column)
+char* obi_column_formatted_infos(OBIDMS_column_p column, bool detailed)
 {
-	char* column_infos;
-	char* elt_names;
-
-	column_infos = malloc(1024 * sizeof(char));
+	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;
 }
 
@@ -2480,7 +2555,6 @@ 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

@@ -77,6 +77,8 @@ typedef struct OBIDMS_column_header {
 	OBIType_t			stored_data_type;		    						/**< Type of the data that is actually stored in the data
 															 	 	 	 	 *   part of the column.
 															 	 	 	 	 */
+	bool                dict_column;										/**< Whether the column contains dictionary-like values.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
 	bool				tuples;												/**< A boolean indicating whether the column contains indices referring to indexed tuples.
 																			 */
 	bool				to_eval;											/**< A boolean indicating whether the column contains expressions that should be evaluated
@@ -249,6 +251,7 @@ size_t obi_calculate_header_size(index_t nb_elements_per_line, int64_t elts_name
  * @param elements_names The names of the elements with ';' as separator (no terminal ';'),
  *                       NULL or "" if the default names are to be used ("0\01\02\0...\0n").
  * @param elt_names_formatted Whether the separator for the elements names is ';' (false), or '\0' (true, as formatted by format_elements_names()).
+ * @param dict_column A boolean indicating whether the column should contain dictionary-like values.
  * @param tuples A boolean indicating whether the column should contain indices referring to indexed tuples.
  * @param to_eval A boolean indicating whether the column contains expressions that should be evaluated
  *                (typically OBI_STR columns containing character strings to be evaluated by Python).
@@ -271,6 +274,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p     dms,
 								  index_t      nb_elements_per_line,
 								  char*        elements_names,
 								  bool		   elt_names_formatted,
+								  bool         dict_column,
 								  bool         tuples,
 								  bool         to_eval,
 								  const char*  indexer_name,
@@ -505,12 +509,37 @@ index_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const cha
 char* obi_get_elements_names(OBIDMS_column_p column);
 
 
-// TODO
-//char* obi_get_formatted_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);
 
 
-// TODO
-//char* obi_column_formatted_infos(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);
 
 
 /**

src/obisig.h

@@ -25,7 +25,7 @@
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  *
  */
-bool volatile keep_running;
+extern bool volatile keep_running;
 void sig_handler(int signum);
 
 

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;
 		}
 	}
@@ -1128,6 +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");
@@ -1193,7 +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");
@@ -1653,7 +1712,7 @@ Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_cl
 		// If there is a new line selection, build it by combining it with the one from the view to clone if there is one
 		else if (line_selection != NULL)
 		{
-			view->line_selection = obi_create_column(view->dms, LINES_COLUMN_NAME, OBI_IDX, 0, 1, NULL, false, false, false, NULL, NULL, -1, NULL);
+			view->line_selection = obi_create_column(view->dms, LINES_COLUMN_NAME, OBI_IDX, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, NULL);
 			if ((view->line_selection) == NULL)
 			{
 				obidebug(1, "\nError creating a column corresponding to a line selection");
@@ -1803,6 +1862,7 @@ Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_cl
 									false,
 									false,
 									false,
+									false,
 									NULL,
 									NULL,
 									-1,
@@ -1844,6 +1904,7 @@ 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)
@@ -1870,19 +1931,19 @@ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p v
 	if ((view_to_clone == NULL) && create_default_columns)
 	{
 		// Adding sequence column
-		if (obi_view_add_column(view, NUC_SEQUENCE_COLUMN, -1, NULL, OBI_SEQ, 0, 1, NULL, false, false, false, NULL, NULL, -1, "{}", true) < 0)	// discuss using same indexer "NUC_SEQ_INDEXER"
+		if (obi_view_add_column(view, NUC_SEQUENCE_COLUMN, -1, NULL, OBI_SEQ, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, "{}", true) < 0)	// discuss using same indexer "NUC_SEQ_INDEXER"
 		{
 			obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
 			return NULL;
 		}
 		// Adding id column
-		if (obi_view_add_column(view, ID_COLUMN, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, NULL, NULL, -1, "{}", true) < 0)
+		if (obi_view_add_column(view, ID_COLUMN, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, "{}", true) < 0)
 		{
 			obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
 			return NULL;
 		}
 		// Adding definition column
-		if (obi_view_add_column(view, DEFINITION_COLUMN, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, NULL, NULL, -1, "{}", true) < 0)
+		if (obi_view_add_column(view, DEFINITION_COLUMN, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, "{}", true) < 0)
 		{
 			obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
 			return NULL;
@@ -1891,11 +1952,15 @@ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p v
 		if (quality_column)
 		{
 			associated_nuc_column = obi_view_get_column(view, NUC_SEQUENCE_COLUMN);
-			if (obi_view_add_column(view, QUALITY_COLUMN, -1, NULL, OBI_QUAL, 0, 1, NULL, false, false, false, NULL, (associated_nuc_column->header)->name, (associated_nuc_column->header)->version, "{}", true) < 0)		// TODO discuss automatic association
+			if (obi_view_add_column(view, QUALITY_COLUMN, -1, NULL, OBI_QUAL, 0, 1, NULL, false, false, false, false, NULL, (associated_nuc_column->header)->name, (associated_nuc_column->header)->version, "{}", true) < 0)		// TODO discuss automatic association
 			{
 				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;
 		}
 	}
 
@@ -1922,7 +1987,7 @@ 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;
@@ -2212,7 +2277,7 @@ 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,
@@ -2220,6 +2285,7 @@ int obi_view_add_column(Obiview_p    view,
 						index_t      nb_elements_per_line,
 						char*        elements_names,
 						bool         elt_names_formatted,
+						bool         dict_column,
 						bool		 tuples,
 						bool         to_eval,
 						const char*  indexer_name,
@@ -2302,7 +2368,7 @@ int obi_view_add_column(Obiview_p    view,
 	// Open or create the column
 	if (create)
 	{	// Create column
-		column = obi_create_column(view->dms, column_name, data_type, nb_lines, nb_elements_per_line, elements_names, elt_names_formatted, tuples, to_eval, indexer_name, associated_column_name, associated_column_version, comments);
+		column = obi_create_column(view->dms, column_name, data_type, nb_lines, nb_elements_per_line, elements_names, elt_names_formatted, dict_column, tuples, to_eval, indexer_name, associated_column_name, associated_column_version, comments);
 		if (column == NULL)
 		{
 			obidebug(1, "\nError creating a column to add to a view");
@@ -2541,6 +2607,144 @@ 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;
@@ -3028,7 +3232,7 @@ int obi_create_auto_count_column(Obiview_p view)
 		return -1;
 	}
 
-	if (obi_view_add_column(view, COUNT_COLUMN, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, "{}", true) < 0)
+	if (obi_view_add_column(view, COUNT_COLUMN, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, "{}", true) < 0)
 	{
 		obidebug(1, "Error adding an automatic count column in a view");
 		return -1;
@@ -3080,7 +3284,7 @@ int obi_create_auto_id_column(Obiview_p view, const char* prefix)
 	}
 
 	// Create the new ID column
-	if (obi_view_add_column(view, ID_COLUMN, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, NULL, NULL, -1, "{}", true) < 0)
+	if (obi_view_add_column(view, ID_COLUMN, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, "{}", true) < 0)
 	{
 		obidebug(1, "Error adding an automatic ID column in a view");
 		return -1;

src/obiview.h

@@ -30,54 +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 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 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 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.
-                                	 	  	  	 */
+ 	 	 	 	 	 	 	 	 	 	 	 	    *    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.
+                                	 	  	  	    */
 
 
 /**
@@ -398,6 +400,7 @@ Obiview_p obi_open_view(OBIDMS_p dms, const char* view_name);
  * @param elements_names The names of the elements with ';' as separator (no terminal ';'),
  * 						 if the column is created; NULL or "" if the default names are to be used ("0\01\02\0...\0n").
  * @param elt_names_formatted Whether the separator for the elements names is ';' (false), or '\0' (true, as formatted by format_elements_names()).
+ * @param dict_column Whether the column contains dictionary-like values.
  * @param tuples A boolean indicating whether the column should contain indices referring to indexed tuples.
  * @param to_eval A boolean indicating whether the column contains expressions that should be evaluated
  *                (typically OBI_STR columns containing character strings to be evaluated by Python).
@@ -406,7 +409,7 @@ 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.
@@ -416,7 +419,7 @@ 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,
@@ -424,6 +427,7 @@ int obi_view_add_column(Obiview_p    view,
 						index_t      nb_elements_per_line,
 						char*        elements_names,
 						bool         elt_names_formatted,
+						bool         dict_column,
 						bool         tuples,
 						bool         to_eval,
 						const char*  indexer_name,
@@ -519,6 +523,39 @@ 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.
  *