mmagnus / rna-tools

def get_parser():

    parser = argparse.ArgumentParser(

        description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)

    #parser.add_argument('-', "--", help="", default="")

    parser.add_argument('--save-to-file', help='<pdb>.fa', action='store_true')

    parser.add_argument('--compact',

                        help=textwrap.dedent("""with --get-seq, get it in compact view'

$ rna_pdb_tools.py --get-seq --compact *.pdb

# 20_Bujnicki_1

ACCCGCAAGGCCGACGGCGCCGCCGCUGGUGCAAGUCCAGCCACGCUUCGGCGUGGGCGCUCAUGGGU # A:1-68

# 20_Bujnicki_2

ACCCGCAAGGCCGACGGCGCCGCCGCUGGUGCAAGUCCAGCCACGCUUCGGCGUGGGCGCUCAUGGGU # A:1-68

# 20_Bujnicki_3

ACCCGCAAGGCCGACGGCGCCGCCGCUGGUGCAAGUCCAGCCACGCUUCGGCGUGGGCGCUCAUGGGU # A:1-68

# 20_Bujnicki_4

"""), action='store_true')

    parser.add_argument('--color-seq', help='color seq, works with --get-seq', action='store_true')

    parser.add_argument('--chain-first', help="", action='store_true')

    parser.add_argument('--fasta',

                        help= textwrap.dedent("""with --get-seq, show sequences in fasta format,

can be combined with --compact (mind, chains will be separated with ' ' in one line)

$ rna_pdb_tools.py --get-seq --fasta --compact input/20_Bujnicki_1.pdb

> 20_Bujnicki_1

ACCCGCAAGGCCGACGGC GCCGCCGCUGGUGCAAGUCCAGCCACGCUUCGGCGUGGGCGCUCAUGGGU

"""), action='store_true')

    parser.add_argument('--oneline', help="", action='store_true')

    parser.add_argument('--uniq', help=textwrap.dedent("""

rna_pdb_tools.py --get-seq --uniq '[:5]' --compact --chain-first * | sort

A:1-121        ACCUUGCGCAACUGGCGAAUCCUGGGGCUGCCGCCGGCAGUACCC...CA # rp13nc3295_min.out.1

A:1-123        ACCUUGCGCGACUGGCGAAUCCUGAAGCUGCUUUGAGCGGCUUCG...AG # rp13cp0016_min.out.1

A:1-123        ACCUUGCGCGACUGGCGAAUCCUGAAGCUGCUUUGAGCGGCUUCG...AG # zcp_6537608a_ALL-000001_AA

A:1-45 57-71   GGGUCGUGACUGGCGAACAGGUGGGAAACCACCGGGGAGCGACCCGCCGCCCGCCUGGGC # solution

"""))

    parser.add_argument('--renum-atoms', help='renumber atoms, tested with --get-seq',

                         action='store_true')

    parser.add_argument("-v", "--verbose",

                        action="store_true", help="be verbose")

    parser.add_argument("file", help="", default="") # nargs='+')

    return parser

if __name__ == '__main__':

   return l

def get_parser():

    parser = argparse.ArgumentParser(

        description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)

    parser.add_argument('-t',"--target",

                         help="target file")

    parser.add_argument('--result', #default='out.rmsd',

                         help="result file")

    parser.add_argument('--ignore-files', default='aligned', help="use to ignore files, .e.g. with 'aligned'")

    parser.add_argument('--suffix', default='aligned', help="used with --saved, by default: aligned")

    parser.add_argument('--way', help="e.g., backbone+sugar")

    parser.add_argument('--triple-mode', help="same crazy strategy to align triples", action="store_true")

    parser.add_argument('--column-name', help="name column for rmsd, by default 'rmsd', but can also be a name of the target file",

                        default="rmsd")

    parser.add_argument("-s", "--save", action="store_true", help="set suffix with --suffix, by default: aligned")

    parser.add_argument('files', help='files', nargs='+')

    parser.add_argument("--debug", action="store_true")

    parser.add_argument("--sort", action="store_true", help='sort results based on rmsd (ascending)')

    return parser

# main

if __name__ == '__main__':

import argparse

import os

def get_parser():

    parser = argparse.ArgumentParser(

        description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)

    parser.add_argument('csv1', help="", default="")

    parser.add_argument('--sep1', help="default is ,; can be also '\t'", default=",")

    parser.add_argument('csv2', help="", default="")

    parser.add_argument('--sep2', help="default is ,; can be also '\t'", default=",")

    parser.add_argument('mergeon', help="merge on column", default="")

    parser.add_argument('--how', help="inner | left | right | outer, default inner", default="inner")

    parser.add_argument('--validate', help="default: one_to_one", default="one_to_one")

    parser.add_argument("-v", "--verbose",

                        action="store_true", help="be verbose")

    parser.add_argument('--output', help="output csv", default="merged.csv")

    parser.add_argument('--force-writing-output',  action="store_true")

    return parser

if __name__ == '__main__':