123 lines
4.3 KiB
Cython
Executable File
123 lines
4.3 KiB
Cython
Executable File
#cython: language_level=3
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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 addMinimalOutputOption
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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 str2bytes
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from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
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from obitools3.dms.view.view cimport View
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from obitools3.dms.capi.obiview cimport NUC_SEQUENCE_COLUMN, REVERSE_SEQUENCE_COLUMN, \
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QUALITY_COLUMN, REVERSE_QUALITY_COLUMN
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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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import time
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import sys
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from cpython.exc cimport PyErr_CheckSignals
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__title__="Concatenate views."
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def addOptions(parser):
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addMinimalOutputOption(parser)
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group=parser.add_argument_group('obi cat specific options')
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group.add_argument("-c",
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action="append", dest="cat:views_to_cat",
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metavar="<VIEW_NAME>",
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default=[],
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type=str,
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help="URI of a view to concatenate. (e.g. 'my_dms/my_view'). "
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"Several -c options can be used on the same "
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"command line.")
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def run(config):
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DMS.obi_atexit()
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logger("info", "obi cat")
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# Open the views to concatenate
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iview_list = []
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idms_list = []
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total_len = 0
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remove_qual = False
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remove_rev_qual = False
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v_type = View_NUC_SEQS
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for v_uri in config["cat"]["views_to_cat"]:
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input = open_uri(v_uri)
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if input is None:
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raise Exception("Could not read input view")
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i_dms = input[0]
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i_view = input[1]
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if input[2] != View_NUC_SEQS: # Check view type (output view is nuc_seqs view if all input view are nuc_seqs view)
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v_type = View
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if QUALITY_COLUMN not in i_view: # Check if keep quality column in output view (if all input views have it)
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remove_qual = True
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if REVERSE_QUALITY_COLUMN not in i_view: # same as above for reverse quality
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remove_rev_qual = True
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total_len += len(i_view)
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iview_list.append(i_view)
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idms_list.append(i_dms)
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# Open the output: only the DMS
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output = open_uri(config['obi']['outputURI'],
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input=False,
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newviewtype=v_type)
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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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o_view = output[1]
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# Initialize quality columns and their associated sequence columns if needed
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if not remove_qual:
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if NUC_SEQUENCE_COLUMN not in o_view:
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Column.new_column(o_view, NUC_SEQUENCE_COLUMN, OBI_SEQ)
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Column.new_column(o_view, QUALITY_COLUMN, OBI_QUAL, associated_column_name=NUC_SEQUENCE_COLUMN, associated_column_version=o_view[NUC_SEQUENCE_COLUMN].version)
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if not remove_rev_qual:
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Column.new_column(o_view, REVERSE_SEQUENCE_COLUMN, OBI_SEQ)
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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)
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# Initialize the progress bar
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pb = ProgressBar(total_len, config, seconde=5)
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i = 0
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for v in iview_list:
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for l in v:
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PyErr_CheckSignals()
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pb(i)
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o_view[i] = l
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i+=1
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# Deletes quality columns if needed
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if QUALITY_COLUMN in o_view and remove_qual :
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o_view.delete_column(QUALITY_COLUMN)
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if REVERSE_QUALITY_COLUMN in o_view and remove_rev_qual :
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o_view.delete_column(REVERSE_QUALITY_COLUMN)
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pb(i, force=True)
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print("", file=sys.stderr)
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# Save command config in DMS comments
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command_line = " ".join(sys.argv[1:])
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o_view.write_config(config, "cat", command_line, input_dms_name=[d.name for d in idms_list], input_view_name=[v.name for v in iview_list])
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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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for d in idms_list:
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d.close()
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o_dms.close()
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logger("info", "Done.")
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