Python: made all commands handle output to buffer object (e.g. stdout)

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:
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
-        temporary_view_name = final_o_view_name
+        if type(output_0)==BufferedWriter:
-        i=0
+            o_dms = i_dms
-        while temporary_view_name in i_dms:  # Making sure view name is unique in input DMS
+        o_view_name = b"temp"
-            temporary_view_name = final_o_view_name+b"_"+str2bytes(str(i))
+        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')
 
@@ -171,13 +174,29 @@ def run(config):
     if output is None:
         raise Exception("Could not create output view")
 
-    view = output[1]
+    output_0 = output[0]
+    o_dms = output[0]
     
-    Column.new_column(view, QUALITY_COLUMN, OBI_QUAL)   #TODO output URI quality option?
+    # 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:
+        o_view = output[1]
+        Column.new_column(o_view, QUALITY_COLUMN, OBI_QUAL)
 
     # Initialize the progress bar
-    pb = ProgressBar(entries_len, config, seconde=5)
+    if config['obi']['noprogressbar'] == False:
-    
+        pb = ProgressBar(entries_len, config)
+    else:
+        pb = None
+         
     #if config['alignpairedend']['trueali']:
     #    kmer_ali = False
     #    aligner = buildAlignment
@@ -202,11 +221,12 @@ 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]
@@ -227,24 +247,37 @@ def run(config):
     
         i+=1
 
-    pb(i, force=True)
+    if pb is not None:
-    print("", file=sys.stderr)
+        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)
+    o_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_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:
@@ -290,7 +303,7 @@ def run(config):
             i+=1
         View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], i_view_name, imported_view_name)
         i_view = o_dms[imported_view_name]
-        
+
     # Clone output view from input view
     o_view = i_view.clone(o_view_name)
     if o_view is None:
@@ -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)
+    if pb is not None:
-    print("", file=sys.stderr)
+        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
+    # stdout output: write to buffer
-    if i_dms != o_dms:
+    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:
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
-        temporary_view_name = final_o_view_name
+        temporary_view_name = b"temp"
         i=0
         while temporary_view_name in i_dms:  # Making sure view name is unique in input DMS
-            temporary_view_name = final_o_view_name+b"_"+str2bytes(str(i))
+            temporary_view_name = temporary_view_name+b"_"+str2bytes(str(i))
             i+=1
         o_view_name = temporary_view_name
+        if type(output_0)==BufferedWriter:
+            o_dms = i_dms
     else:
         o_view_name = final_o_view_name
 
@@ -80,22 +86,29 @@ def run(config):
     input_dms_name.append(config['obi']['taxoURI'].split("/")[-3])
     input_view_name.append("taxonomy/"+config['obi']['taxoURI'].split("/")[-1])
     comments = View.print_config(config, "build_ref_db", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
-
+    
     if build_reference_db(i_dms.name_with_full_path, tobytes(i_view_name), tobytes(taxonomy_name), tobytes(o_view_name), comments, config['build_ref_db']['threshold']) < 0:
         raise Exception("Error building a reference database")
     
     # If the input and output DMS are not the same, export result view to output DMS
     if i_dms != o_dms:
         View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, final_o_view_name)
-    
+
+    # stdout output: write to buffer
+    if type(output_0)==BufferedWriter:
+        logger("info", "Printing to output...")
+        o_view = o_dms[o_view_name]
+        o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
+        o_view.close()
+
     # Save command config in DMS comments
     o_dms.record_command_line(command_line)
 
     #print("\n\nOutput view:\n````````````", file=sys.stderr)
     #print(repr(o_dms[final_o_view_name]), file=sys.stderr)
 
-    # If the input and the output DMS are different, delete the temporary result view in the input DMS
+    # If 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:
+    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

@@ -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
  
@@ -76,53 +77,70 @@ 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 type(output_0) != BufferedWriter: 
-        if NUC_SEQUENCE_COLUMN not in o_view:
+        if not remove_qual:
-            Column.new_column(o_view, NUC_SEQUENCE_COLUMN, OBI_SEQ)
+            if NUC_SEQUENCE_COLUMN not in o_view:
-        Column.new_column(o_view, QUALITY_COLUMN, OBI_QUAL, associated_column_name=NUC_SEQUENCE_COLUMN, associated_column_version=o_view[NUC_SEQUENCE_COLUMN].version)    
+                Column.new_column(o_view, NUC_SEQUENCE_COLUMN, OBI_SEQ)
-    if not remove_rev_qual:
+            Column.new_column(o_view, QUALITY_COLUMN, OBI_QUAL, associated_column_name=NUC_SEQUENCE_COLUMN, associated_column_version=o_view[NUC_SEQUENCE_COLUMN].version)    
-        Column.new_column(o_view, REVERSE_SEQUENCE_COLUMN, OBI_SEQ)
+        if not remove_rev_qual:
-        Column.new_column(o_view, REVERSE_QUALITY_COLUMN, OBI_QUAL, associated_column_name=REVERSE_SEQUENCE_COLUMN, associated_column_version=o_view[REVERSE_SEQUENCE_COLUMN].version)
+            Column.new_column(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 = {}
+    if type(output_0)==BufferedWriter: 
-    for v in iview_list:
+        dict_cols = {}
-        for coln in v.keys():
+        for v in iview_list:
-            if v[coln].nb_elements_per_line > 1:
+            for coln in v.keys():
-                if coln not in dict_cols:
+                if v[coln].nb_elements_per_line > 1:
-                    dict_cols[coln] = {}
+                    if coln not in dict_cols:
-                    dict_cols[coln]['eltnames'] = set(v[coln].elements_names)
+                        dict_cols[coln] = {}
-                    dict_cols[coln]['nbelts'] = v[coln].nb_elements_per_line
+                        dict_cols[coln]['eltnames'] = set(v[coln].elements_names)
-                    dict_cols[coln]['obitype'] = v[coln].data_type_int
+                        dict_cols[coln]['nbelts'] = v[coln].nb_elements_per_line
-                else:
+                        dict_cols[coln]['obitype'] = v[coln].data_type_int
-                    dict_cols[coln]['eltnames'] = set(v[coln].elements_names + list(dict_cols[coln]['eltnames']))
+                    else:
-                    dict_cols[coln]['nbelts'] = len(dict_cols[coln]['eltnames'])
+                        dict_cols[coln]['eltnames'] = set(v[coln].elements_names + list(dict_cols[coln]['eltnames']))
-    for coln in dict_cols:
+                        dict_cols[coln]['nbelts'] = len(dict_cols[coln]['eltnames'])
-        Column.new_column(o_view, coln, dict_cols[coln]['obitype'], 
+        for coln in dict_cols:
-                          nb_elements_per_line=dict_cols[coln]['nbelts'], elements_names=list(dict_cols[coln]['eltnames']))
+            Column.new_column(o_view, coln, dict_cols[coln]['obitype'], 
+                              nb_elements_per_line=dict_cols[coln]['nbelts'], elements_names=list(dict_cols[coln]['eltnames']))
     
     # Initialize the progress bar
-    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 entry in v:
             PyErr_CheckSignals()
-            pb(i)
+            if pb is not None:
-            o_view[i] = l
+                pb(i)
+            if type(output_0)==BufferedWriter: 
+                rep = repr(entry)
+                output_0.write(str2bytes(rep)+b"\n")
+            else:
+                o_view[i] = entry
             i+=1
 
     # Deletes quality columns if needed
-    if QUALITY_COLUMN in o_view and remove_qual :
+    if type(output_0)!=BufferedWriter: 
-        o_view.delete_column(QUALITY_COLUMN)
+        if QUALITY_COLUMN in o_view and remove_qual :
-    if REVERSE_QUALITY_COLUMN in o_view and remove_rev_qual :
+            o_view.delete_column(QUALITY_COLUMN)
-        o_view.delete_column(REVERSE_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:])

python/obitools3/commands/clean.pyx

@@ -4,13 +4,14 @@ from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
 from obitools3.dms.dms cimport DMS
 from obitools3.dms.view import RollbackException
 from obitools3.dms.capi.obiclean cimport obi_clean
-from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption
+from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption, addNoProgressBarOption
 from obitools3.uri.decode import open_uri
 from obitools3.apps.config import logger
 from obitools3.utils cimport tobytes, str2bytes
 from obitools3.dms.view.view cimport View
 from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
 
+from io import BufferedWriter
 import sys
 
 
@@ -21,7 +22,8 @@ def addOptions(parser):
 
     addMinimalInputOption(parser)
     addMinimalOutputOption(parser)
- 
+    addNoProgressBarOption(parser)
+    
     group = parser.add_argument_group('obi clean specific options')
 
     group.add_argument('--distance', '-d',
@@ -88,17 +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:
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
-        temporary_view_name = final_o_view_name
+        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
         
@@ -116,15 +121,22 @@ def run(config):
     # If the input and output DMS are not the same, export result view to output DMS
     if i_dms != o_dms:
         View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, final_o_view_name)
-    
+
+    # stdout output: write to buffer
+    if type(output_0)==BufferedWriter:
+        logger("info", "Printing to output...")
+        o_view = o_dms[o_view_name]
+        o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
+        o_view.close()
+
     # Save command config in DMS comments
     o_dms.record_command_line(command_line)
 
     #print("\n\nOutput view:\n````````````", file=sys.stderr)
     #print(repr(o_dms[final_o_view_name]), file=sys.stderr)
 
-    # If the input and the output DMS are different, delete the temporary result view in the input DMS
+    # If 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:
+    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/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')
@@ -169,11 +171,20 @@ def run(config):
     if output is None:
         raise Exception("Could not create output")
     o_dms = output[0]
+    output_0 = output[0]
     o_dms_name = output[0].name
     o_view_name = output[1]
 
     # Read taxonomy name    
     taxonomy_name = config['obi']['taxoURI'].split("/")[-1]   # Robust in theory
+
+    # If stdout output create a temporary view in the input dms that will be deleted afterwards.
+    if type(output_0)==BufferedWriter:
+        o_dms = i_dms
+        o_view_name = b"temp"
+        while o_view_name in i_dms:   # Making sure view name is unique in input DMS
+            o_view_name = o_view_name+b"_"+str2bytes(str(i))
+            i+=1
     
     # Save command config in View comments
     command_line = " ".join(sys.argv[1:])
@@ -201,10 +212,21 @@ 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')
 
@@ -75,17 +77,19 @@ 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 
+    # If stdout output or the input and output DMS are not the same, create a temporary view that will be exported and deleted.
-    # the right DMS and deleted in the other afterwards.
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
-    if i_dms != o_dms:
+        temporary_view_name = b"temp"
-        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))
+            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
 
@@ -120,11 +124,18 @@ 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 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:
+    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 :

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")
  
@@ -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]
+    output_0 = output[0]
-    o_view_name = o_view_name_final
+    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
+    # If stdout output or the input and output DMS are not the same, create a temporary view that will be exported and deleted afterwards.
-    # to output DMS, making sure the temporary view name is unique in the input DMS 
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
-    if i_dms != o_dms:
+        temporary_view_name = b"temp"
         i=0
-        while o_view_name in i_dms:
+        while temporary_view_name in i_dms:  # Making sure view name is unique in input DMS
-            o_view_name = o_view_name_final+b"_"+str2bytes(str(i))
+            temporary_view_name = temporary_view_name+b"_"+str2bytes(str(i))
-            i+=1        
+            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}
@@ -349,9 +361,10 @@ def run(config):
      
             if good :
                 selection.append(i)
-    
+   
-    pb(len(i_view), force=True)
+    if pb is not None:
-    print("", file=sys.stderr)
+        pb(len(i_view), force=True)
+        print("", file=sys.stderr)
 
     # Create output view with the line selection
     try:
@@ -375,14 +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)
+        View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, final_o_view_name)
-        o_view = o_dms[o_view_name_final]
+        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 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:
+    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

@@ -4,14 +4,15 @@ from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
 from obitools3.dms import DMS
 from obitools3.dms.view.view cimport View, Line_selection
 from obitools3.uri.decode import open_uri
-from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption
+from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption, addNoProgressBarOption
 from obitools3.dms.view import RollbackException
 from obitools3.apps.config import logger
 from obitools3.utils cimport str2bytes
 
 import time
 import sys
- 
+from io import BufferedWriter
+
 from cpython.exc cimport PyErr_CheckSignals
 
 
@@ -22,6 +23,7 @@ def addOptions(parser):
     
     addMinimalInputOption(parser)
     addMinimalOutputOption(parser)
+    addNoProgressBarOption(parser)
 
     group=parser.add_argument_group('obi head specific options')
 
@@ -53,31 +55,41 @@ def run(config):
     if output is None:
         raise Exception("Could not create output view")
     o_dms = output[0]
-    o_view_name_final = output[1]
+    output_0 = output[0]
-    o_view_name = o_view_name_final
+    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
+    # If stdout output or the input and output DMS are not the same, create a temporary view that will be exported and deleted.
-    # to output DMS, making sure the temporary view name is unique in the input DMS 
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
-    if i_dms != o_dms:
+        temporary_view_name = b"temp"
         i=0
-        while o_view_name in i_dms:
+        while temporary_view_name in i_dms:  # Making sure view name is unique in input DMS
-            o_view_name = o_view_name_final+b"_"+str2bytes(str(i))
+            temporary_view_name = temporary_view_name+b"_"+str2bytes(str(i))
-            i+=1        
+            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)
+    if pb is not None:
-    print("", file=sys.stderr)
+        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)
+        View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, final_o_view_name)
-        o_view = o_dms[o_view_name_final]
+        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 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:
+    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

@@ -47,6 +47,8 @@ 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"
  
@@ -130,7 +132,7 @@ 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:
@@ -178,7 +180,7 @@ def run(config):
         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) :
@@ -243,7 +245,7 @@ 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:

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
@@ -14,13 +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
+from io import BufferedWriter
 
 
 #REVERSE_SEQ_COLUMN_NAME = b"REVERSE_SEQUENCE"      # used by alignpairedend tool
@@ -34,7 +35,8 @@ def addOptions(parser):
 
     addMinimalInputOption(parser)
     addMinimalOutputOption(parser)
- 
+    addNoProgressBarOption(parser)
+    
     group = parser.add_argument_group('obi ngsfilter specific options')
 
     group.add_argument('-t','--info-view',
@@ -539,7 +541,8 @@ def run(config):
         raise Exception("Could not open input reads")
     if input[2] != View_NUC_SEQS:
         raise NotImplementedError('obi ngsfilter only works on NUC_SEQS views')
-
+    i_dms = input[0]
+    
     if "reverse" in config["ngsfilter"]:
         
         forward = input[1]        
@@ -580,8 +583,19 @@ def run(config):
     if output is None:
         raise Exception("Could not create output view")
     
+    o_dms = output[0]
+    output_0 = output[0]
     o_view = output[1]
     
+    # If stdout output, create a temporary view in the input dms that will be deleted afterwards.
+    if type(output_0)==BufferedWriter:
+        o_dms = i_dms
+        o_view_name = b"temp"
+        while o_view_name in i_dms:   # Making sure view name is unique in input DMS
+            o_view_name = o_view_name+b"_"+str2bytes(str(i))
+            i+=1
+        o_view = View_NUC_SEQS.new(i_dms, o_view_name)
+
     # Open the view containing the informations about the tags and the primers
     info_input = open_uri(config['ngsfilter']['info_view'])
     if info_input is None:
@@ -602,7 +616,10 @@ 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 +653,8 @@ 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:
@@ -660,8 +678,9 @@ def run(config):
         else:
             raise RollbackException("obi ngsfilter error, rollbacking view: "+str(e), o_view)
     
-    pb(i, force=True)
+    if pb is not None:
-    print("", file=sys.stderr)
+        pb(i, force=True)
+        print("", file=sys.stderr)
 
     # Save command config in View and DMS comments
     command_line = " ".join(sys.argv[1:])
@@ -670,13 +689,23 @@ 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)
+    # If stdout output, delete the temporary result view in the input DMS
-    output[0].close(force=True)
+    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')
 
@@ -59,7 +61,7 @@ def addOptions(parser):
 
 
 def line_cmp(line, key, pb): 
-    pb   
+    pb
     if line[key] is None:
         return NULL_VALUE[line.view[key].data_type_int]
     else:
@@ -86,20 +88,28 @@ def run(config):
     if output is None:
         raise Exception("Could not create output view")
     o_dms = output[0]
-    o_view_name_final = output[1]
+    output_0 = output[0]
-    o_view_name = o_view_name_final
+    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
+    # If stdout output or the input and output DMS are not the same, create a temporary view that will be exported and deleted.
-    # to output DMS, making sure the temporary view name is unique in the input DMS 
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
-    if i_dms != o_dms:
+        temporary_view_name = b"temp"
         i=0
-        while o_view_name in i_dms:
+        while temporary_view_name in i_dms:  # Making sure view name is unique in input DMS
-            o_view_name = o_view_name_final+b"_"+str2bytes(str(i))
+            temporary_view_name = temporary_view_name+b"_"+str2bytes(str(i))
-            i+=1        
+            i+=1
+        o_view_name = temporary_view_name
+        if type(output_0)==BufferedWriter:
+            o_dms = i_dms
+    else:
+        o_view_name = final_o_view_name
 
     # Initialize the progress bar
-    pb = ProgressBar(len(i_view), config, seconde=5)
+    if config['obi']['noprogressbar'] == False:
-    
+        pb = ProgressBar(len(i_view), config)
+    else:
+        pb = None
+
     keys = config['sort']['keys']
         
     selection = Line_selection(i_view)
@@ -110,10 +120,14 @@ def run(config):
     
     for k in keys:  # TODO order?
         PyErr_CheckSignals()
-        selection.sort(key=lambda line_idx: line_cmp(i_view[line_idx], k, pb(line_idx)), reverse=config['sort']['reverse'])
+        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'])
-    pb(len(i_view), force=True)
+        else:
-    print("", file=sys.stderr)
+            selection.sort(key=lambda line_idx: line_cmp(i_view[line_idx], k, None), reverse=config['sort']['reverse'])
+    
+    if pb is not None:
+        pb(len(i_view), force=True)
+        print("", file=sys.stderr)
 
     # Create output view with the sorted line selection
     try:
@@ -132,16 +146,23 @@ def run(config):
     # and delete the temporary view in the input DMS
     if i_dms != o_dms:
         o_view.close()
-        View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, o_view_name_final)
+        View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, final_o_view_name)
-        o_view = o_dms[o_view_name_final]
+        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 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:
+    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]
+    output_0 = output[0]
-    o_view_name = o_view_name_final
+    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
+    # If stdout output or the input and output DMS are not the same, create a temporary view that will be exported and deleted.
-    # to output DMS, making sure the temporary view name is unique in the input DMS 
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
-    if i_dms != o_dms:
+        temporary_view_name = b"temp"
         i=0
-        while o_view_name in i_dms:
+        while temporary_view_name in i_dms:  # Making sure view name is unique in input DMS
-            o_view_name = o_view_name_final+b"_"+str2bytes(str(i))
+            temporary_view_name = temporary_view_name+b"_"+str2bytes(str(i))
-            i+=1        
+            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)
+    if pb is not None:
-    print("", file=sys.stderr)
+        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)
+        View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, final_o_view_name)
-        o_view = o_dms[o_view_name_final]
+        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 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:
+    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/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 
@@ -415,12 +424,17 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, di
     o_count_col = o_view[COUNT_COLUMN]
     if COUNT_COLUMN in view:
         i_count_col = view[COUNT_COLUMN]
+    
+    if pb is not None:
+        pb(len(view), force=True)
+        print("")
         
-    pb(len(view), force=True)
-    print("")
     logger("info", "Second browsing through the input")
+    
     # Initialize the progress bar
-    pb = ProgressBar(len(view), seconde=5)
+    if pb is not None:
+        pb = ProgressBar(len(view))
+        
     o_idx = 0
     total_treated = 0
     
@@ -455,7 +469,9 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, di
 
         for i_idx in merged_sequences:
             PyErr_CheckSignals()
-            pb(total_treated)
+            
+            if pb is not None:
+                pb(total_treated)
  
             i_id = i_id_col[i_idx]
             i_seq = view[i_idx]
@@ -531,7 +547,8 @@ 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:
@@ -579,8 +596,23 @@ 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'])
@@ -591,7 +623,10 @@ 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:
@@ -599,7 +634,8 @@ 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:])
@@ -609,13 +645,23 @@ 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)
+    # If stdout output, delete the temporary result view in the input DMS
-    output[0].close(force=True)
+    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/uri/decode.pyx

@@ -210,10 +210,11 @@ def open_uri(uri,
     
     error = None
     
-    if scheme==b"dms" or \
+    if urib != b"-" and \
-        (scheme==b"" and \
+        (scheme==b"dms" or \
-         (((not input) and "outputformat" not in config["obi"]) or \
+         (scheme==b"" and \
-         (input and "inputformat" not in config["obi"]))):   # TODO maybe not best way
+          (((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:
+        if urip.path == b'-':
-            file = open(urip.path, 'wb')
-        else:
             file = sys.stdout.buffer
+        elif urip.path :
+            file = open(urip.path, 'wb')
         
     if file is not None:
         qualifiers=parse_qs(urip.query)