Code Duplication - mmagnus/rna-tools - Measure and Improve Code Quality continuously with Scrutinizer

Code Duplication Length = 69-72 lines in 2 locations

rna_tools/tools/mq/rna_mq_collect.py 1 location


        pass


def option_parser():
    """Get options or show usage msg.
    """
    description = ''
    version = __version__
    usage = '\t%prog [-m <number_processes>] [-n <native_pdb_filename>] [-s <seq_ss_filename>] [-g <ignore_pdb_filename>] \ \n\t -o <output csv> <dir/*> # [!] no .csv! the file will get version of mqaprna \n\t' + __version__
    parser = OptionParser(description=__doc__,
                              version=version,
                              usage=usage)

    parser.add_option("-q", "--mQapscore",
                     action="store_true", default=False, dest="mqapscore", help="calculate mqapscore")

    parser.add_option("-v", "--verbose",
                     action="store_true", default=False, dest="verbose", help="verbose")

    parser.add_option("--force",
                     action="store_true", default=False)

    parser.add_option("-f", "--no-filename-version",
                     action="store_true", default=False, dest="no_filename_version", help="don't add version of tool to csv filename")


    parser.add_option("-n", "--native_pdb_filename",
                     action="store", type="string", dest="native_pdb_filename", help="native structure in PDB format to calculate RMSD")

    parser.add_option("-m", "--multiprocessing",
                     action="store", type="int", dest="number_processes", default=8,
                      help="set a number of processes, default=8, 0 is no multiprocessing")

    group2 = OptionGroup(parser, "Ignore pdbs, don't have empty lines here! Example",
                        """1xjrA_output3-000142_AA.pdb
                         1xjrA_output3-000208_AA.pdb
                         1xjrA_output3-000166_AA.pdb""")

    group2.add_option("-g", "--ignore-pdbs",
                  action="store", type="string", dest="ignore_pdb_filename")

    group = OptionGroup(parser, "Seq-SS. Example",
                        """>1xjrA
                        GAGUUCACCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAUU
                        .(((((((...((((.((((.....))..))..))).).)))))))""")

    group.add_option("-t", "--methods",
                  action="store", type="string", dest="methods", help=', '.join(['RASP',  'SimRNA', 'AnalyzeGeometry','FARNA', 'QRNA', 'NAST_pyro',
                                                                                 'radius_of_gyration', 'SSAgreement', 'ClashScore', 'RNAkb',
                                                                                 'RNAkb_all', 'FARNA_hires', 'FARNA', 'FARFAR2',
                                                                                 'FARFAR2_hires', 'Dfire', 'RNA3DCNN', 'eSCORE']))

    group.add_option("-s", "--seq-ss",
                  action="store", type="string", dest="seq_ss_filename", help="")

    group.add_option("-o", "--output",
                  action="store", type="string", dest="output", help="output csv file")

    group.add_option("-l", "--list-of-files",
                  action="store", type="string", dest="list_of_files", help="list of files")


    parser.add_option_group(group)
    parser.add_option_group(group2)

    (opt, arguments) = parser.parse_args()

    arguments = [f for f in arguments if f.endswith('.pdb')]

    if len(arguments) == 0:
        parser.print_help()
        print('\n   Curr methods: ', ','.join(methods), end=' ')
        sys.exit(1)

    return arguments, opt


class RunAllDirectory():

rna_tools/tools/mq/rna_mq_collect_tqdm.py 1 location


        pass


def option_parser():
    """Get options or show usage msg.
    """
    description = ''
    version = __version__
    usage = '\t%prog [-m <number_processes>] [-n <native_pdb_filename>] [-s <seq_ss_filename>] [-g <ignore_pdb_filename>] \ \n\t -o <output csv> <dir/*> # [!] no .csv! the file will get version of mqaprna \n\t' + __version__
    parser = OptionParser(description=__doc__,
                              version=version,
                              usage=usage)

    parser.add_option("-q", "--mQapscore",
                     action="store_true", default=False, dest="mqapscore", help="calculate mqapscore")

    parser.add_option("-v", "--verbose",
                     action="store_true", default=False, dest="verbose", help="verbose")

    parser.add_option("-f", "--no-filename-version",
                     action="store_true", default=False, dest="no_filename_version", help="don't add version of tool to csv filename")


    parser.add_option("-n", "--native_pdb_filename",
                     action="store", type="string", dest="native_pdb_filename", help="native structure in PDB format to calculate RMSD")

    parser.add_option("-m", "--multiprocessing",
                     action="store", type="int", dest="number_processes", default=1,
                      help="set a number of processes, default=8, 0 is no multiprocessing")

    group2 = OptionGroup(parser, "Ignore pdbs, don't have empty lines here! Example",
                        """1xjrA_output3-000142_AA.pdb
                         1xjrA_output3-000208_AA.pdb
                         1xjrA_output3-000166_AA.pdb""")

    group2.add_option("-g", "--ignore-pdbs",
                  action="store", type="string", dest="ignore_pdb_filename")

    group = OptionGroup(parser, "Seq-SS. Example",
                        """>1xjrA
                        GAGUUCACCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAUU
                        .(((((((...((((.((((.....))..))..))).).)))))))""")

    group.add_option("-t", "--methods",
                  action="store", type="string", dest="methods", help=', '.join(['RASP',  'SimRNA', 'AnalyzeGeometry','FARNA', 'QRNA', 'NAST_pyro',
                                                                                 'radius_of_gyration', 'SSAgreement', 'ClashScore', 'RNAkb',
                                                                                 'RNAkb_all', 'FARNA_hires', 'FARNA', 'FARFAR2',
                                                                                 'FARFAR2_hires', 'Dfire', 'RNA3DCNN', 'eSCORE']))

    group.add_option("-s", "--seq-ss",
                  action="store", type="string", dest="seq_ss_filename", help="")

    group.add_option("-o", "--output",
                  action="store", type="string", dest="output", help="output csv file")

    group.add_option("-l", "--list-of-files",
                  action="store", type="string", dest="list_of_files", help="list of files")


    parser.add_option_group(group)
    parser.add_option_group(group2)

    (opt, arguments) = parser.parse_args()

    arguments = [f for f in arguments if f.endswith('.pdb')]

    if len(arguments) == 0:
        parser.print_help()
        print('\n   Curr methods: ', ','.join(methods), end=' ')
        sys.exit(1)

    return arguments, opt


class RunAllDirectory():

		@@ 349-420 (lines=72) @@
346		pass
347
348
349		def option_parser():
350		"""Get options or show usage msg.
351		"""
352		description = ''
353		version = __version__
354		usage = '\t%prog [-m <number_processes>] [-n <native_pdb_filename>] [-s <seq_ss_filename>] [-g <ignore_pdb_filename>] \ \n\t -o <output csv> <dir/*> # [!] no .csv! the file will get version of mqaprna \n\t' + __version__
355		parser = OptionParser(description=__doc__,
356		version=version,
357		usage=usage)
358
359		parser.add_option("-q", "--mQapscore",
360		action="store_true", default=False, dest="mqapscore", help="calculate mqapscore")
361
362		parser.add_option("-v", "--verbose",
363		action="store_true", default=False, dest="verbose", help="verbose")
364
365		parser.add_option("--force",
366		action="store_true", default=False)
367
368		parser.add_option("-f", "--no-filename-version",
369		action="store_true", default=False, dest="no_filename_version", help="don't add version of tool to csv filename")
370
371
372		parser.add_option("-n", "--native_pdb_filename",
373		action="store", type="string", dest="native_pdb_filename", help="native structure in PDB format to calculate RMSD")
374
375		parser.add_option("-m", "--multiprocessing",
376		action="store", type="int", dest="number_processes", default=8,
377		help="set a number of processes, default=8, 0 is no multiprocessing")
378
379		group2 = OptionGroup(parser, "Ignore pdbs, don't have empty lines here! Example",
380		"""1xjrA_output3-000142_AA.pdb
381		1xjrA_output3-000208_AA.pdb
382		1xjrA_output3-000166_AA.pdb""")
383
384		group2.add_option("-g", "--ignore-pdbs",
385		action="store", type="string", dest="ignore_pdb_filename")
386
387		group = OptionGroup(parser, "Seq-SS. Example",
388		""">1xjrA
389		GAGUUCACCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAUU
390		.(((((((...((((.((((.....))..))..))).).)))))))""")
391
392		group.add_option("-t", "--methods",
393		action="store", type="string", dest="methods", help=', '.join(['RASP', 'SimRNA', 'AnalyzeGeometry','FARNA', 'QRNA', 'NAST_pyro',
394		'radius_of_gyration', 'SSAgreement', 'ClashScore', 'RNAkb',
395		'RNAkb_all', 'FARNA_hires', 'FARNA', 'FARFAR2',
396		'FARFAR2_hires', 'Dfire', 'RNA3DCNN', 'eSCORE']))
397
398		group.add_option("-s", "--seq-ss",
399		action="store", type="string", dest="seq_ss_filename", help="")
400
401		group.add_option("-o", "--output",
402		action="store", type="string", dest="output", help="output csv file")
403
404		group.add_option("-l", "--list-of-files",
405		action="store", type="string", dest="list_of_files", help="list of files")
406
407
408		parser.add_option_group(group)
409		parser.add_option_group(group2)
410
411		(opt, arguments) = parser.parse_args()
412
413		arguments = [f for f in arguments if f.endswith('.pdb')]
414
415		if len(arguments) == 0:
416		parser.print_help()
417		print('\n Curr methods: ', ','.join(methods), end=' ')
418		sys.exit(1)
419
420		return arguments, opt
421
422
423		class RunAllDirectory():

		@@ 329-397 (lines=69) @@
326		pass
327
328
329		def option_parser():
330		"""Get options or show usage msg.
331		"""
332		description = ''
333		version = __version__
334		usage = '\t%prog [-m <number_processes>] [-n <native_pdb_filename>] [-s <seq_ss_filename>] [-g <ignore_pdb_filename>] \ \n\t -o <output csv> <dir/*> # [!] no .csv! the file will get version of mqaprna \n\t' + __version__
335		parser = OptionParser(description=__doc__,
336		version=version,
337		usage=usage)
338
339		parser.add_option("-q", "--mQapscore",
340		action="store_true", default=False, dest="mqapscore", help="calculate mqapscore")
341
342		parser.add_option("-v", "--verbose",
343		action="store_true", default=False, dest="verbose", help="verbose")
344
345		parser.add_option("-f", "--no-filename-version",
346		action="store_true", default=False, dest="no_filename_version", help="don't add version of tool to csv filename")
347
348
349		parser.add_option("-n", "--native_pdb_filename",
350		action="store", type="string", dest="native_pdb_filename", help="native structure in PDB format to calculate RMSD")
351
352		parser.add_option("-m", "--multiprocessing",
353		action="store", type="int", dest="number_processes", default=1,
354		help="set a number of processes, default=8, 0 is no multiprocessing")
355
356		group2 = OptionGroup(parser, "Ignore pdbs, don't have empty lines here! Example",
357		"""1xjrA_output3-000142_AA.pdb
358		1xjrA_output3-000208_AA.pdb
359		1xjrA_output3-000166_AA.pdb""")
360
361		group2.add_option("-g", "--ignore-pdbs",
362		action="store", type="string", dest="ignore_pdb_filename")
363
364		group = OptionGroup(parser, "Seq-SS. Example",
365		""">1xjrA
366		GAGUUCACCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAUU
367		.(((((((...((((.((((.....))..))..))).).)))))))""")
368
369		group.add_option("-t", "--methods",
370		action="store", type="string", dest="methods", help=', '.join(['RASP', 'SimRNA', 'AnalyzeGeometry','FARNA', 'QRNA', 'NAST_pyro',
371		'radius_of_gyration', 'SSAgreement', 'ClashScore', 'RNAkb',
372		'RNAkb_all', 'FARNA_hires', 'FARNA', 'FARFAR2',
373		'FARFAR2_hires', 'Dfire', 'RNA3DCNN', 'eSCORE']))
374
375		group.add_option("-s", "--seq-ss",
376		action="store", type="string", dest="seq_ss_filename", help="")
377
378		group.add_option("-o", "--output",
379		action="store", type="string", dest="output", help="output csv file")
380
381		group.add_option("-l", "--list-of-files",
382		action="store", type="string", dest="list_of_files", help="list of files")
383
384
385		parser.add_option_group(group)
386		parser.add_option_group(group2)
387
388		(opt, arguments) = parser.parse_args()
389
390		arguments = [f for f in arguments if f.endswith('.pdb')]
391
392		if len(arguments) == 0:
393		parser.print_help()
394		print('\n Curr methods: ', ','.join(methods), end=' ')
395		sys.exit(1)
396
397		return arguments, opt
398
399
400		class RunAllDirectory():

mmagnus / rna-tools

Code Duplication Length = 69-72 lines in 2 locations

rna_tools/tools/mq/rna_mq_collect.py 1 location

rna_tools/tools/mq/rna_mq_collect_tqdm.py 1 location