119 lines
4.5 KiB
Cython
Executable File
119 lines
4.5 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.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, 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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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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group.add_argument('--threshold','-t',
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action="store", dest="build_ref_db:threshold",
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metavar='<THRESHOLD>',
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default=0.0,
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type=float,
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help="Score threshold as a normalized identity, e.g. 0.95 for an identity of 95%%. Default: 0.00"
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" (no threshold).")
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def run(config):
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DMS.obi_atexit()
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logger("info", "obi build_ref_db")
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# Open the input: only the DMS
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input = open_uri(config['obi']['inputURI'],
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dms_only=True)
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if input is None:
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raise Exception("Could not read input")
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i_dms = input[0]
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i_dms_name = input[0].name
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i_view_name = input[1]
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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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dms_only=True)
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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 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 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 = 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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# Read taxonomy name
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taxonomy_name = config['obi']['taxoURI'].split("/")[-1] # Robust in theory
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# Save command config in View comments
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command_line = " ".join(sys.argv[1:])
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input_dms_name=[i_dms_name]
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input_view_name= [i_view_name]
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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 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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i_dms.close(force=True)
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logger("info", "Done.")
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