Python: made all commands handle output to buffer object (e.g. stdout)
This commit is contained in:
Celine Mercier
@ -4,7 +4,7 @@ from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
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from obitools3.dms import DMS
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from obitools3.dms.view.view cimport View
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from obitools3.uri.decode import open_uri
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from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption
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from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption, addNoProgressBarOption
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from obitools3.dms.view import RollbackException
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from obitools3.apps.config import logger
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from obitools3.utils cimport tobytes, str2bytes
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@ -12,6 +12,9 @@ from obitools3.utils cimport tobytes, str2bytes
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from obitools3.dms.capi.obilcsalign cimport obi_lcs_align_one_column, \
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obi_lcs_align_two_columns
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from io import BufferedWriter
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from cpython.exc cimport PyErr_CheckSignals
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import time
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import sys
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@ -23,6 +26,7 @@ def addOptions(parser):
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addMinimalInputOption(parser)
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addMinimalOutputOption(parser)
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addNoProgressBarOption(parser)
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group=parser.add_argument_group('obi align specific options')
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@ -201,20 +205,20 @@ def run(config):
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if output is None:
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raise Exception("Could not create output")
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o_dms = output[0]
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output_0 = output[0]
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o_dms_name = o_dms.name
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final_o_view_name = output[1]
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o_view_name = final_o_view_name
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# If the input and output DMS are not the same, align creating a temporary view in the input dms that will be exported to
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# 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
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# the right DMS and deleted in the other afterwards.
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if i_dms != o_dms:
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temporary_view_name = final_o_view_name
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i=0
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while temporary_view_name in i_dms: # Making sure view name is unique in input DMS
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temporary_view_name = final_o_view_name+b"_"+str2bytes(str(i))
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if i_dms != o_dms or type(output_0)==BufferedWriter:
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if type(output_0)==BufferedWriter:
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o_dms = i_dms
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o_view_name = b"temp"
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while o_view_name in i_dms: # Making sure view name is unique in input DMS
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o_view_name = o_view_name+b"_"+str2bytes(str(i))
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i+=1
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o_view_name = temporary_view_name
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else:
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o_view_name = final_o_view_name
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# Save command config in View comments
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command_line = " ".join(sys.argv[1:])
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@ -263,8 +267,15 @@ def run(config):
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View.delete_view(i_dms, i_view_name_2)
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i_dms_2.close()
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# stdout output: write to buffer
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if type(output_0)==BufferedWriter:
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logger("info", "Printing to output...")
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o_view = o_dms[o_view_name]
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o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
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o_view.close()
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# If the input and the output DMS are different, delete the temporary result view in the input DMS
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if i_dms != o_dms:
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if i_dms != o_dms or type(output_0)==BufferedWriter:
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View.delete_view(i_dms, o_view_name)
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o_dms.close(force=True)
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@ -6,7 +6,7 @@ from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
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from obitools3.dms.column.column cimport Column
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from obitools3.dms.capi.obiview cimport QUALITY_COLUMN
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from obitools3.dms.capi.obitypes cimport OBI_QUAL
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from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption
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from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption, addNoProgressBarOption
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from obitools3.uri.decode import open_uri
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from obitools3.apps.config import logger
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from obitools3.libalign._qsassemble import QSolexaReverseAssemble
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@ -15,7 +15,9 @@ from obitools3.libalign._solexapairend import buildConsensus, buildJoinedSequenc
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from obitools3.dms.obiseq cimport Nuc_Seq
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from obitools3.libalign.shifted_ali cimport Kmer_similarity, Ali_shifted
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from obitools3.dms.capi.obiview cimport REVERSE_SEQUENCE_COLUMN, REVERSE_QUALITY_COLUMN
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from obitools3.utils cimport str2bytes
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from io import BufferedWriter
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import sys
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import os
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@ -29,6 +31,7 @@ def addOptions(parser):
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addMinimalInputOption(parser)
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addMinimalOutputOption(parser)
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addNoProgressBarOption(parser)
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group = parser.add_argument_group('obi alignpairedend specific options')
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@ -171,13 +174,29 @@ def run(config):
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if output is None:
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raise Exception("Could not create output view")
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view = output[1]
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output_0 = output[0]
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o_dms = output[0]
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Column.new_column(view, QUALITY_COLUMN, OBI_QUAL) #TODO output URI quality option?
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# stdout output: create temporary view
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if type(output_0)==BufferedWriter:
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i_dms = forward.dms # using any dms
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o_dms = i_dms
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i=0
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o_view_name = b"temp"
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while o_view_name in i_dms: # Making sure view name is unique in input DMS
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o_view_name = o_view_name+b"_"+str2bytes(str(i))
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i+=1
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o_view = View_NUC_SEQS.new(o_dms, o_view_name, quality=True)
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else:
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o_view = output[1]
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Column.new_column(o_view, QUALITY_COLUMN, OBI_QUAL)
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# Initialize the progress bar
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pb = ProgressBar(entries_len, config, seconde=5)
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if config['obi']['noprogressbar'] == False:
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pb = ProgressBar(entries_len, config)
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else:
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pb = None
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#if config['alignpairedend']['trueali']:
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# kmer_ali = False
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# aligner = buildAlignment
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@ -202,11 +221,12 @@ def run(config):
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i = 0
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for ali in ba:
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pb(i)
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if pb is not None:
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pb(i)
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PyErr_CheckSignals()
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consensus = view[i]
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consensus = o_view[i]
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if not two_views:
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seqF = entries[i]
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@ -227,24 +247,37 @@ def run(config):
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i+=1
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pb(i, force=True)
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print("", file=sys.stderr)
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if pb is not None:
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pb(i, force=True)
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print("", file=sys.stderr)
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if kmer_ali :
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aligner.free()
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# Save command config in View and DMS comments
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command_line = " ".join(sys.argv[1:])
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view.write_config(config, "alignpairedend", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
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output[0].record_command_line(command_line)
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o_view.write_config(config, "alignpairedend", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
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o_dms.record_command_line(command_line)
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#print("\n\nOutput view:\n````````````", file=sys.stderr)
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#print(repr(view), file=sys.stderr)
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# stdout output: write to buffer
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if type(output_0)==BufferedWriter:
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logger("info", "Printing to output...")
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o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
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o_view.close()
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# If stdout output, delete the temporary imported view used to create the final file
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if type(output_0)==BufferedWriter:
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View_NUC_SEQS.delete_view(o_dms, o_view_name)
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output_0.close()
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# Close all DMS
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input[0].close(force=True)
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if two_views:
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rinput[0].close(force=True)
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output[0].close(force=True)
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o_dms.close(force=True)
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logger("info", "Done.")
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@ -4,11 +4,12 @@ from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
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from obitools3.dms import DMS
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from obitools3.dms.view.view cimport View, Line_selection
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from obitools3.uri.decode import open_uri
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from obitools3.apps.optiongroups import addMinimalInputOption, addTaxonomyOption, addMinimalOutputOption
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from obitools3.apps.optiongroups import addMinimalInputOption, addTaxonomyOption, addMinimalOutputOption, addNoProgressBarOption
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from obitools3.dms.view import RollbackException
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from functools import reduce
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from obitools3.apps.config import logger
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from obitools3.utils cimport tobytes, str2bytes
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from io import BufferedWriter
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from obitools3.dms.capi.obiview cimport NUC_SEQUENCE_COLUMN, \
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ID_COLUMN, \
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DEFINITION_COLUMN, \
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@ -34,6 +35,7 @@ def addOptions(parser):
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addMinimalInputOption(parser)
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addTaxonomyOption(parser)
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addMinimalOutputOption(parser)
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addNoProgressBarOption(parser)
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group=parser.add_argument_group('obi annotate specific options')
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@ -278,8 +280,19 @@ def run(config):
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if output is None:
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raise Exception("Could not create output view")
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o_dms = output[0]
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output_0 = output[0]
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o_view_name = output[1]
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# stdout output: create temporary view
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if type(output_0)==BufferedWriter:
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o_dms = i_dms
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i=0
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o_view_name = b"temp"
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while o_view_name in i_dms: # Making sure view name is unique in output DMS
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o_view_name = o_view_name+b"_"+str2bytes(str(i))
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i+=1
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imported_view_name = o_view_name
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# If the input and output DMS are not the same, import the input view in the output DMS before cloning it to modify it
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# (could be the other way around: clone and modify in the input DMS then import the new view in the output DMS)
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if i_dms != o_dms:
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@ -290,7 +303,7 @@ def run(config):
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i+=1
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View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], i_view_name, imported_view_name)
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i_view = o_dms[imported_view_name]
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# Clone output view from input view
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o_view = i_view.clone(o_view_name)
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if o_view is None:
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@ -307,7 +320,10 @@ def run(config):
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taxo = None
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# Initialize the progress bar
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pb = ProgressBar(len(o_view), config, seconde=5)
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if config['obi']['noprogressbar'] == False:
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pb = ProgressBar(len(o_view), config)
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else:
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pb = None
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try:
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@ -346,14 +362,16 @@ def run(config):
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sequenceTagger = sequenceTaggerGenerator(config, taxo=taxo)
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for i in range(len(o_view)):
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PyErr_CheckSignals()
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pb(i)
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if pb is not None:
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pb(i)
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sequenceTagger(o_view[i])
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except Exception, e:
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raise RollbackException("obi annotate error, rollbacking view: "+str(e), o_view)
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pb(i, force=True)
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print("", file=sys.stderr)
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if pb is not None:
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pb(i, force=True)
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print("", file=sys.stderr)
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# Save command config in View and DMS comments
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command_line = " ".join(sys.argv[1:])
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@ -363,13 +381,19 @@ def run(config):
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input_dms_name.append(config['obi']['taxoURI'].split("/")[-3])
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input_view_name.append("taxonomy/"+config['obi']['taxoURI'].split("/")[-1])
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o_view.write_config(config, "annotate", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
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output[0].record_command_line(command_line)
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o_dms.record_command_line(command_line)
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#print("\n\nOutput view:\n````````````", file=sys.stderr)
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#print(repr(o_view), file=sys.stderr)
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# If the input and the output DMS are different, delete the temporary imported view used to create the final view
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if i_dms != o_dms:
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# stdout output: write to buffer
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if type(output_0)==BufferedWriter:
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logger("info", "Printing to output...")
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o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
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o_view.close()
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# If the input and the output DMS are different or if stdout output, delete the temporary imported view used to create the final view
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if i_dms != o_dms or type(output_0)==BufferedWriter:
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View.delete_view(o_dms, imported_view_name)
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o_dms.close(force=True)
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i_dms.close(force=True)
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@ -4,14 +4,16 @@ from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
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from obitools3.dms.dms cimport DMS
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from obitools3.dms.view import RollbackException
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from obitools3.dms.capi.build_reference_db cimport build_reference_db
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from obitools3.apps.optiongroups import addMinimalInputOption, addTaxonomyOption, addMinimalOutputOption
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from obitools3.apps.optiongroups import addMinimalInputOption, addTaxonomyOption, addMinimalOutputOption, addNoProgressBarOption
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from obitools3.uri.decode import open_uri
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from obitools3.apps.config import logger
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from obitools3.utils cimport tobytes, str2bytes
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from obitools3.dms.view.view cimport View
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from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
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from io import BufferedWriter
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import sys
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from cpython.exc cimport PyErr_CheckSignals
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__title__="Tag a set of sequences for PCR and sequencing errors identification"
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@ -22,6 +24,7 @@ def addOptions(parser):
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addMinimalInputOption(parser)
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addTaxonomyOption(parser)
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addMinimalOutputOption(parser)
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addNoProgressBarOption(parser)
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group = parser.add_argument_group('obi build_ref_db specific options')
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@ -56,17 +59,20 @@ def run(config):
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if output is None:
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raise Exception("Could not create output")
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o_dms = output[0]
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output_0 = output[0]
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final_o_view_name = output[1]
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# If the input and output DMS are not the same, build the database creating a temporary view that will be exported to
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# 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
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# the right DMS and deleted in the other afterwards.
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if i_dms != o_dms:
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temporary_view_name = final_o_view_name
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if i_dms != o_dms or type(output_0)==BufferedWriter:
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temporary_view_name = b"temp"
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i=0
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while temporary_view_name in i_dms: # Making sure view name is unique in input DMS
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temporary_view_name = final_o_view_name+b"_"+str2bytes(str(i))
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temporary_view_name = temporary_view_name+b"_"+str2bytes(str(i))
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i+=1
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o_view_name = temporary_view_name
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if type(output_0)==BufferedWriter:
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o_dms = i_dms
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else:
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o_view_name = final_o_view_name
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@ -80,22 +86,29 @@ def run(config):
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input_dms_name.append(config['obi']['taxoURI'].split("/")[-3])
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input_view_name.append("taxonomy/"+config['obi']['taxoURI'].split("/")[-1])
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comments = View.print_config(config, "build_ref_db", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
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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:
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raise Exception("Error building a reference database")
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# If the input and output DMS are not the same, export result view to output DMS
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if i_dms != o_dms:
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View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, final_o_view_name)
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# stdout output: write to buffer
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if type(output_0)==BufferedWriter:
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logger("info", "Printing to output...")
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o_view = o_dms[o_view_name]
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o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
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o_view.close()
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# Save command config in DMS comments
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o_dms.record_command_line(command_line)
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#print("\n\nOutput view:\n````````````", file=sys.stderr)
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#print(repr(o_dms[final_o_view_name]), file=sys.stderr)
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# If the input and the output DMS are different, delete the temporary result view in the input DMS
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if i_dms != o_dms:
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# If the input and the output DMS are different or if stdout output, delete the temporary imported view used to create the final view
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if i_dms != o_dms or type(output_0)==BufferedWriter:
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View.delete_view(i_dms, o_view_name)
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o_dms.close(force=True)
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@ -15,6 +15,7 @@ from obitools3.dms.capi.obiview cimport NUC_SEQUENCE_COLUMN, REVERSE_SEQUENCE_CO
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from obitools3.dms.capi.obitypes cimport OBI_SEQ, OBI_QUAL
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from obitools3.dms.column.column cimport Column
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from io import BufferedWriter
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import time
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import sys
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@ -76,53 +77,70 @@ def run(config):
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if output is None:
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raise Exception("Could not create output view")
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o_dms = output[0]
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output_0 = output[0]
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o_view = output[1]
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# 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 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']))
|
||||
|
||||
# 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)
|
||||
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
|
||||
|
||||
# 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)
|
||||
|
||||
pb(i, force=True)
|
||||
print("", file=sys.stderr)
|
||||
if type(output_0)!=BufferedWriter:
|
||||
if QUALITY_COLUMN in o_view and remove_qual :
|
||||
o_view.delete_column(QUALITY_COLUMN)
|
||||
if REVERSE_QUALITY_COLUMN in o_view and remove_rev_qual :
|
||||
o_view.delete_column(REVERSE_QUALITY_COLUMN)
|
||||
|
||||
if pb is not None:
|
||||
pb(i, force=True)
|
||||
print("", file=sys.stderr)
|
||||
|
||||
# Save command config in DMS comments
|
||||
command_line = " ".join(sys.argv[1:])
|
||||
|
||||
@ -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:
|
||||
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
|
||||
|
||||
@ -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 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)
|
||||
|
||||
|
||||
@ -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)
|
||||
|
||||
|
||||
@ -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
|
||||
# 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
|
||||
|
||||
@ -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 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)
|
||||
|
||||
|
||||
@ -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 :
|
||||
|
||||
@ -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]
|
||||
o_view_name = o_view_name_final
|
||||
|
||||
# If the input and output DMS are not the same, create output view in input DMS first, then export it
|
||||
# to output DMS, making sure the temporary view name is unique in the input DMS
|
||||
if i_dms != o_dms:
|
||||
output_0 = output[0]
|
||||
final_o_view_name = output[1]
|
||||
|
||||
# If stdout output or the input and output DMS are not the same, create a temporary view that will be exported and deleted afterwards.
|
||||
if i_dms != o_dms or type(output_0)==BufferedWriter:
|
||||
temporary_view_name = b"temp"
|
||||
i=0
|
||||
while o_view_name in i_dms:
|
||||
o_view_name = o_view_name_final+b"_"+str2bytes(str(i))
|
||||
i+=1
|
||||
while temporary_view_name in i_dms: # Making sure view name is unique in input DMS
|
||||
temporary_view_name = temporary_view_name+b"_"+str2bytes(str(i))
|
||||
i+=1
|
||||
o_view_name = temporary_view_name
|
||||
if type(output_0)==BufferedWriter:
|
||||
o_dms = i_dms
|
||||
else:
|
||||
o_view_name = final_o_view_name
|
||||
|
||||
if 'taxoURI' in config['obi'] and config['obi']['taxoURI'] is not None:
|
||||
taxo_uri = open_uri(config["obi"]["taxoURI"])
|
||||
@ -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)
|
||||
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:
|
||||
@ -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)
|
||||
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)
|
||||
|
||||
@ -4,14 +4,15 @@ from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
|
||||
from obitools3.dms import DMS
|
||||
from obitools3.dms.view.view cimport View, Line_selection
|
||||
from obitools3.uri.decode import open_uri
|
||||
from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption
|
||||
from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption, addNoProgressBarOption
|
||||
from obitools3.dms.view import RollbackException
|
||||
from obitools3.apps.config import logger
|
||||
from obitools3.utils cimport str2bytes
|
||||
|
||||
import time
|
||||
import sys
|
||||
|
||||
from io import BufferedWriter
|
||||
|
||||
from cpython.exc cimport PyErr_CheckSignals
|
||||
|
||||
|
||||
@ -22,6 +23,7 @@ def addOptions(parser):
|
||||
|
||||
addMinimalInputOption(parser)
|
||||
addMinimalOutputOption(parser)
|
||||
addNoProgressBarOption(parser)
|
||||
|
||||
group=parser.add_argument_group('obi head specific options')
|
||||
|
||||
@ -53,31 +55,41 @@ def run(config):
|
||||
if output is None:
|
||||
raise Exception("Could not create output view")
|
||||
o_dms = output[0]
|
||||
o_view_name_final = output[1]
|
||||
o_view_name = o_view_name_final
|
||||
output_0 = output[0]
|
||||
final_o_view_name = output[1]
|
||||
|
||||
# If the input and output DMS are not the same, create output view in input DMS first, then export it
|
||||
# to output DMS, making sure the temporary view name is unique in the input DMS
|
||||
if i_dms != o_dms:
|
||||
# If stdout output or the input and output DMS are not the same, create a temporary view that will be exported and deleted.
|
||||
if i_dms != o_dms or type(output_0)==BufferedWriter:
|
||||
temporary_view_name = b"temp"
|
||||
i=0
|
||||
while o_view_name in i_dms:
|
||||
o_view_name = o_view_name_final+b"_"+str2bytes(str(i))
|
||||
i+=1
|
||||
while temporary_view_name in i_dms: # Making sure view name is unique in input DMS
|
||||
temporary_view_name = temporary_view_name+b"_"+str2bytes(str(i))
|
||||
i+=1
|
||||
o_view_name = temporary_view_name
|
||||
if type(output_0)==BufferedWriter:
|
||||
o_dms = i_dms
|
||||
else:
|
||||
o_view_name = final_o_view_name
|
||||
|
||||
n = min(config['head']['count'], len(i_view))
|
||||
|
||||
# Initialize the progress bar
|
||||
pb = ProgressBar(n, config, seconde=5)
|
||||
if config['obi']['noprogressbar'] == False:
|
||||
pb = ProgressBar(n, config)
|
||||
else:
|
||||
pb = None
|
||||
|
||||
selection = Line_selection(i_view)
|
||||
|
||||
for i in range(n):
|
||||
PyErr_CheckSignals()
|
||||
pb(i)
|
||||
if pb is not None:
|
||||
pb(i)
|
||||
selection.append(i)
|
||||
|
||||
pb(i, force=True)
|
||||
print("", file=sys.stderr)
|
||||
if pb is not None:
|
||||
pb(i, force=True)
|
||||
print("", file=sys.stderr)
|
||||
|
||||
# Create output view with the line selection
|
||||
try:
|
||||
@ -94,14 +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)
|
||||
|
||||
@ -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:
|
||||
|
||||
@ -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)
|
||||
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:])
|
||||
@ -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)
|
||||
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)
|
||||
|
||||
@ -4,7 +4,7 @@ from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
|
||||
from obitools3.dms import DMS
|
||||
from obitools3.dms.view.view cimport View, Line_selection
|
||||
from obitools3.uri.decode import open_uri
|
||||
from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption
|
||||
from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption, addNoProgressBarOption
|
||||
from obitools3.dms.view import RollbackException
|
||||
from obitools3.apps.config import logger
|
||||
from obitools3.utils cimport str2bytes
|
||||
@ -24,6 +24,7 @@ from obitools3.dms.capi.obitypes cimport OBI_BOOL, \
|
||||
import time
|
||||
import sys
|
||||
from cpython.exc cimport PyErr_CheckSignals
|
||||
from io import BufferedWriter
|
||||
|
||||
|
||||
NULL_VALUE = {OBI_BOOL: OBIBool_NA,
|
||||
@ -42,6 +43,7 @@ def addOptions(parser):
|
||||
|
||||
addMinimalInputOption(parser)
|
||||
addMinimalOutputOption(parser)
|
||||
addNoProgressBarOption(parser)
|
||||
|
||||
group=parser.add_argument_group('obi sort specific options')
|
||||
|
||||
@ -59,7 +61,7 @@ def addOptions(parser):
|
||||
|
||||
|
||||
def line_cmp(line, key, pb):
|
||||
pb
|
||||
pb
|
||||
if line[key] is None:
|
||||
return NULL_VALUE[line.view[key].data_type_int]
|
||||
else:
|
||||
@ -86,20 +88,28 @@ def run(config):
|
||||
if output is None:
|
||||
raise Exception("Could not create output view")
|
||||
o_dms = output[0]
|
||||
o_view_name_final = output[1]
|
||||
o_view_name = o_view_name_final
|
||||
output_0 = output[0]
|
||||
final_o_view_name = output[1]
|
||||
|
||||
# If the input and output DMS are not the same, create output view in input DMS first, then export it
|
||||
# to output DMS, making sure the temporary view name is unique in the input DMS
|
||||
if i_dms != o_dms:
|
||||
# If stdout output or the input and output DMS are not the same, create a temporary view that will be exported and deleted.
|
||||
if i_dms != o_dms or type(output_0)==BufferedWriter:
|
||||
temporary_view_name = b"temp"
|
||||
i=0
|
||||
while o_view_name in i_dms:
|
||||
o_view_name = o_view_name_final+b"_"+str2bytes(str(i))
|
||||
i+=1
|
||||
while temporary_view_name in i_dms: # Making sure view name is unique in input DMS
|
||||
temporary_view_name = temporary_view_name+b"_"+str2bytes(str(i))
|
||||
i+=1
|
||||
o_view_name = temporary_view_name
|
||||
if type(output_0)==BufferedWriter:
|
||||
o_dms = i_dms
|
||||
else:
|
||||
o_view_name = final_o_view_name
|
||||
|
||||
# Initialize the progress bar
|
||||
pb = ProgressBar(len(i_view), config, seconde=5)
|
||||
|
||||
if config['obi']['noprogressbar'] == False:
|
||||
pb = ProgressBar(len(i_view), config)
|
||||
else:
|
||||
pb = None
|
||||
|
||||
keys = config['sort']['keys']
|
||||
|
||||
selection = Line_selection(i_view)
|
||||
@ -110,10 +120,14 @@ def run(config):
|
||||
|
||||
for k in keys: # TODO order?
|
||||
PyErr_CheckSignals()
|
||||
selection.sort(key=lambda line_idx: line_cmp(i_view[line_idx], k, pb(line_idx)), reverse=config['sort']['reverse'])
|
||||
|
||||
pb(len(i_view), force=True)
|
||||
print("", file=sys.stderr)
|
||||
if pb is not None:
|
||||
selection.sort(key=lambda line_idx: line_cmp(i_view[line_idx], k, pb(line_idx)), reverse=config['sort']['reverse'])
|
||||
else:
|
||||
selection.sort(key=lambda line_idx: line_cmp(i_view[line_idx], k, None), reverse=config['sort']['reverse'])
|
||||
|
||||
if pb is not None:
|
||||
pb(len(i_view), force=True)
|
||||
print("", file=sys.stderr)
|
||||
|
||||
# Create output view with the sorted line selection
|
||||
try:
|
||||
@ -132,16 +146,23 @@ def run(config):
|
||||
# and delete the temporary view in the input DMS
|
||||
if i_dms != o_dms:
|
||||
o_view.close()
|
||||
View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, o_view_name_final)
|
||||
o_view = o_dms[o_view_name_final]
|
||||
View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, final_o_view_name)
|
||||
o_view = o_dms[final_o_view_name]
|
||||
|
||||
# stdout output: write to buffer
|
||||
if type(output_0)==BufferedWriter:
|
||||
logger("info", "Printing to output...")
|
||||
o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
|
||||
o_view.close()
|
||||
|
||||
#print("\n\nOutput view:\n````````````", file=sys.stderr)
|
||||
#print(repr(o_view), file=sys.stderr)
|
||||
|
||||
# If the input and the output DMS are different, delete the temporary imported view used to create the final view
|
||||
if i_dms != o_dms:
|
||||
# If the input and the output DMS are different or if stdout output, delete the temporary imported view used to create the final view
|
||||
if i_dms != o_dms or type(output_0)==BufferedWriter:
|
||||
View.delete_view(i_dms, o_view_name)
|
||||
o_dms.close(force=True)
|
||||
|
||||
i_dms.close(force=True)
|
||||
|
||||
logger("info", "Done.")
|
||||
|
||||
@ -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()
|
||||
|
||||
@ -4,7 +4,7 @@ from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
|
||||
from obitools3.dms import DMS
|
||||
from obitools3.dms.view.view cimport View, Line_selection
|
||||
from obitools3.uri.decode import open_uri
|
||||
from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption
|
||||
from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption, addNoProgressBarOption
|
||||
from obitools3.dms.view import RollbackException
|
||||
from obitools3.apps.config import logger
|
||||
from obitools3.utils cimport str2bytes
|
||||
@ -12,6 +12,7 @@ from obitools3.utils cimport str2bytes
|
||||
import time
|
||||
import sys
|
||||
from cpython.exc cimport PyErr_CheckSignals
|
||||
from io import BufferedWriter
|
||||
|
||||
|
||||
__title__="Keep the N last lines of a view."
|
||||
@ -21,6 +22,7 @@ def addOptions(parser):
|
||||
|
||||
addMinimalInputOption(parser)
|
||||
addMinimalOutputOption(parser)
|
||||
addNoProgressBarOption(parser)
|
||||
|
||||
group=parser.add_argument_group('obi tail specific options')
|
||||
|
||||
@ -52,31 +54,41 @@ def run(config):
|
||||
if output is None:
|
||||
raise Exception("Could not create output view")
|
||||
o_dms = output[0]
|
||||
o_view_name_final = output[1]
|
||||
o_view_name = o_view_name_final
|
||||
output_0 = output[0]
|
||||
final_o_view_name = output[1]
|
||||
|
||||
# If the input and output DMS are not the same, create output view in input DMS first, then export it
|
||||
# to output DMS, making sure the temporary view name is unique in the input DMS
|
||||
if i_dms != o_dms:
|
||||
# If stdout output or the input and output DMS are not the same, create a temporary view that will be exported and deleted.
|
||||
if i_dms != o_dms or type(output_0)==BufferedWriter:
|
||||
temporary_view_name = b"temp"
|
||||
i=0
|
||||
while o_view_name in i_dms:
|
||||
o_view_name = o_view_name_final+b"_"+str2bytes(str(i))
|
||||
i+=1
|
||||
while temporary_view_name in i_dms: # Making sure view name is unique in input DMS
|
||||
temporary_view_name = temporary_view_name+b"_"+str2bytes(str(i))
|
||||
i+=1
|
||||
o_view_name = temporary_view_name
|
||||
if type(output_0)==BufferedWriter:
|
||||
o_dms = i_dms
|
||||
else:
|
||||
o_view_name = final_o_view_name
|
||||
|
||||
start = max(len(i_view) - config['tail']['count'], 0)
|
||||
|
||||
# Initialize the progress bar
|
||||
pb = ProgressBar(len(i_view) - start, config, seconde=5)
|
||||
if config['obi']['noprogressbar'] == False:
|
||||
pb = ProgressBar(len(i_view) - start, config)
|
||||
else:
|
||||
pb = None
|
||||
|
||||
selection = Line_selection(i_view)
|
||||
|
||||
for i in range(start, len(i_view)):
|
||||
PyErr_CheckSignals()
|
||||
pb(i)
|
||||
if pb is not None:
|
||||
pb(i)
|
||||
selection.append(i)
|
||||
|
||||
pb(i, force=True)
|
||||
print("", file=sys.stderr)
|
||||
if pb is not None:
|
||||
pb(i, force=True)
|
||||
print("", file=sys.stderr)
|
||||
|
||||
# Save command config in View comments
|
||||
command_line = " ".join(sys.argv[1:])
|
||||
@ -97,14 +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)
|
||||
|
||||
@ -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)
|
||||
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.")
|
||||
|
||||
|
||||
@ -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 urip.path == b'-':
|
||||
file = sys.stdout.buffer
|
||||
elif urip.path :
|
||||
file = open(urip.path, 'wb')
|
||||
|
||||
if file is not None:
|
||||
qualifiers=parse_qs(urip.query)
|
||||
|
||||
Reference in New Issue
Block a user