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

Code Duplication Length = 13-16 lines in 7 locations

rna_tools/tools/rna_rosetta/rna_rosetta_check_progress.py 1 location


    return out, err


def get_parser():
    parser = argparse.ArgumentParser(
        description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
    parser.add_argument('dir', default=RNA_ROSETTA_RUN_ROOT_DIR_MODELING,
                        help="""directory with rosetta runs, define by RNA_ROSETTA_RUN_ROOT_DIR_MODELING
right now: \n""" + RNA_ROSETTA_RUN_ROOT_DIR_MODELING)
    parser.add_argument('-v', '--verbose',
                        action='store_true', help="be verbose")
    parser.add_argument('-m', '--min-only', action='store_true',
                        help="check only for mo folder")
    parser.add_argument('-s', '--select',
                        help="select for analysis only jobs with this phrase, .e.g., evoseq_", default='')

    parser.add_argument('-k', '--kill', action='store_true', help="""kill (qdel) jobs if your reach
limit (nstruc) of structure that you want, right now is %i structures""" % RNA_ROSETTA_NSTRUC)
    return parser


if __name__ == '__main__':

rna_tools/tools/rna_alignment/utils/rna_alignment_get_species.py 1 location


import mysql.connector


def get_parser():
    parser = argparse.ArgumentParser(
        description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)

    parser.add_argument("-v", "--verbose",
                        action="store_true", help="be verbose")
    parser.add_argument("--debug", action="store_true")
    parser.add_argument('--id-width', type=int, default=50, help="define width of ids, trim species name when longer than this")
    parser.add_argument('--evo-mapping')
    parser.add_argument('--evo-mapping-default', action="store_true")
    parser.add_argument('--one', action="store_true")
    parser.add_argument('--osfn', help="cache file")
    parser.add_argument('--rfam', action="store_true")
    parser.add_argument("alignment", help="alignment")
    return parser


def ungap(x):

rna_tools/tools/rna_alignment/utils/rna_alignment_merge_by_species.py 1 location


import sys


def get_parser():
    parser = argparse.ArgumentParser(
        description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)

    parser.add_argument("-v", "--verbose",
                        action="store_true", help="be verbose")
    parser.add_argument('--id-width', type=int, default=50)
    parser.add_argument('--evo-mapping')
    parser.add_argument('--evo-mapping-default', action="store_true")
    parser.add_argument('--one', action="store_true")
    parser.add_argument('--u5', action="store_true")
    parser.add_argument('--calc-energy', action="store_true")
    parser.add_argument("alignment")
    parser.add_argument("alignment2")
    return parser


def ungap(x):

rna_tools/tools/pefx/pefx.py 1 location


import re


def get_parser():
    parser = argparse.ArgumentParser(
        description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)

    parser.add_argument('-d', "--dryrun",
                        action="store_true", help="dry run", default=False)

    parser.add_argument('-p', '--path', help="", default='')
    parser.add_argument('-f', '--folder-only', help="",  action="store_true")
    parser.add_argument('-c', '--case', help="only one case, for test")
    parser.add_argument("-v", "--verbose",
                        action="store_true", help="be verbose")
    parser.add_argument('cmd')
    return parser


def sort_nicely(l):

rna_tools/tools/rna_alignment/utils/rna_alignment_calc_energy.py 1 location


def ungap(x):
    return x.replace('-', '')

def get_parser():
    parser = argparse.ArgumentParser(
        description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
    parser.add_argument("--debug", action="store_true")
    parser.add_argument('--one', help="one only for the first seq", action="store_true")
    parser.add_argument('--method', help="mcfold or rnastructure_CycleFold", default="mcfold")#rnastructure_CycleFold") #mcfold")
    parser.add_argument('--csv')
    parser.add_argument('--loop-seq', action="store_true")
    parser.add_argument('--template')
    parser.add_argument('--flanks', help="GC be default") #, default='GC')
    parser.add_argument('-v', '--verbose', action="store_true")
    parser.add_argument('alignment', help="an alignment in the Stockholm format")
    return parser


if __name__ == '__main__':

rna_tools/tools/automatix/rp13_automatix.py 1 location


import glob


def get_parser():
    parser = argparse.ArgumentParser(
        description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)

    parser.add_argument('-d', "--dryrun",
                        action="store_true", help="dry run", default=False)

    parser.add_argument('-p', '--path', help="", default='')
    parser.add_argument('-c', '--case', help="only one case, for test")
    parser.add_argument('-e', '--exe', help="only one case, for test")
    parser.add_argument("-v", "--verbose",
                        action="store_true", help="be verbose")
    return parser

def exe(cmd, dryrun=False):
    print(cmd)

rna_tools/tools/automatix/automatix.py 1 location


import glob


def get_parser():
    parser = argparse.ArgumentParser(
        description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)

    parser.add_argument('-d', "--dryrun",
                        action="store_true", help="dry run", default=False)

    parser.add_argument('-p', '--path', help="", default='')
    parser.add_argument('-c', '--case', help="only one case, for test", default="*")
    parser.add_argument('-e', '--exe', help="only one case, for test")
    parser.add_argument("-v", "--verbose",
                        action="store_true", help="be verbose")
    return parser

def exe(cmd, dryrun=False):
    print(cmd)

		@@ 41-56 (lines=16) @@
38		return out, err
39
40
41		def get_parser():
42		parser = argparse.ArgumentParser(
43		description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
44		parser.add_argument('dir', default=RNA_ROSETTA_RUN_ROOT_DIR_MODELING,
45		help="""directory with rosetta runs, define by RNA_ROSETTA_RUN_ROOT_DIR_MODELING
46		right now: \n""" + RNA_ROSETTA_RUN_ROOT_DIR_MODELING)
47		parser.add_argument('-v', '--verbose',
48		action='store_true', help="be verbose")
49		parser.add_argument('-m', '--min-only', action='store_true',
50		help="check only for mo folder")
51		parser.add_argument('-s', '--select',
52		help="select for analysis only jobs with this phrase, .e.g., evoseq_", default='')
53
54		parser.add_argument('-k', '--kill', action='store_true', help="""kill (qdel) jobs if your reach
55		limit (nstruc) of structure that you want, right now is %i structures""" % RNA_ROSETTA_NSTRUC)
56		return parser
57
58
59		if __name__ == '__main__':

		@@ 51-65 (lines=15) @@
48		import mysql.connector
49
50
51		def get_parser():
52		parser = argparse.ArgumentParser(
53		description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
54
55		parser.add_argument("-v", "--verbose",
56		action="store_true", help="be verbose")
57		parser.add_argument("--debug", action="store_true")
58		parser.add_argument('--id-width', type=int, default=50, help="define width of ids, trim species name when longer than this")
59		parser.add_argument('--evo-mapping')
60		parser.add_argument('--evo-mapping-default', action="store_true")
61		parser.add_argument('--one', action="store_true")
62		parser.add_argument('--osfn', help="cache file")
63		parser.add_argument('--rfam', action="store_true")
64		parser.add_argument("alignment", help="alignment")
65		return parser
66
67
68		def ungap(x):

		@@ 23-37 (lines=15) @@
20		import sys
21
22
23		def get_parser():
24		parser = argparse.ArgumentParser(
25		description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
26
27		parser.add_argument("-v", "--verbose",
28		action="store_true", help="be verbose")
29		parser.add_argument('--id-width', type=int, default=50)
30		parser.add_argument('--evo-mapping')
31		parser.add_argument('--evo-mapping-default', action="store_true")
32		parser.add_argument('--one', action="store_true")
33		parser.add_argument('--u5', action="store_true")
34		parser.add_argument('--calc-energy', action="store_true")
35		parser.add_argument("alignment")
36		parser.add_argument("alignment2")
37		return parser
38
39
40		def ungap(x):

		@@ 19-32 (lines=14) @@
16		import re
17
18
19		def get_parser():
20		parser = argparse.ArgumentParser(
21		description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
22
23		parser.add_argument('-d', "--dryrun",
24		action="store_true", help="dry run", default=False)
25
26		parser.add_argument('-p', '--path', help="", default='')
27		parser.add_argument('-f', '--folder-only', help="", action="store_true")
28		parser.add_argument('-c', '--case', help="only one case, for test")
29		parser.add_argument("-v", "--verbose",
30		action="store_true", help="be verbose")
31		parser.add_argument('cmd')
32		return parser
33
34
35		def sort_nicely(l):

		@@ 89-101 (lines=13) @@
86		def ungap(x):
87		return x.replace('-', '')
88
89		def get_parser():
90		parser = argparse.ArgumentParser(
91		description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
92		parser.add_argument("--debug", action="store_true")
93		parser.add_argument('--one', help="one only for the first seq", action="store_true")
94		parser.add_argument('--method', help="mcfold or rnastructure_CycleFold", default="mcfold")#rnastructure_CycleFold") #mcfold")
95		parser.add_argument('--csv')
96		parser.add_argument('--loop-seq', action="store_true")
97		parser.add_argument('--template')
98		parser.add_argument('--flanks', help="GC be default") #, default='GC')
99		parser.add_argument('-v', '--verbose', action="store_true")
100		parser.add_argument('alignment', help="an alignment in the Stockholm format")
101		return parser
102
103
104		if __name__ == '__main__':

		@@ 13-25 (lines=13) @@
10		import glob
11
12
13		def get_parser():
14		parser = argparse.ArgumentParser(
15		description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
16
17		parser.add_argument('-d', "--dryrun",
18		action="store_true", help="dry run", default=False)
19
20		parser.add_argument('-p', '--path', help="", default='')
21		parser.add_argument('-c', '--case', help="only one case, for test")
22		parser.add_argument('-e', '--exe', help="only one case, for test")
23		parser.add_argument("-v", "--verbose",
24		action="store_true", help="be verbose")
25		return parser
26
27		def exe(cmd, dryrun=False):
28		print(cmd)

mmagnus / rna-tools

Code Duplication Length = 13-16 lines in 7 locations

rna_tools/tools/rna_rosetta/rna_rosetta_check_progress.py 1 location

rna_tools/tools/rna_alignment/utils/rna_alignment_get_species.py 1 location

rna_tools/tools/rna_alignment/utils/rna_alignment_merge_by_species.py 1 location

rna_tools/tools/pefx/pefx.py 1 location

rna_tools/tools/rna_alignment/utils/rna_alignment_calc_energy.py 1 location

rna_tools/tools/automatix/rp13_automatix.py 1 location

rna_tools/tools/automatix/automatix.py 1 location