Source code for padmet_utils.exploration.get_pwy_from_rxn

# -*- coding: utf-8 -*-
"""
Description:
    From a file containing a list of reaction, return the pathways where these reactions 
    are involved.
    ex: if rxn-a in pwy-x => return, pwy-x; all rxn ids in pwy-x; all rxn ids in pwy-x FROM the list; ratio

::
    
    usage:
        get_pwy_from_rxn.py --reaction_file=FILE --padmetRef=FILE  --output=FILE
    
    options:
        -h --help     Show help.
        --reaction_file=FILE    pathname of the file containing the reactions id, 1/line 
        --padmetRef=FILE    pathname of the padmet representing the database.
        --output=FILE    pathname of the file with line = pathway id, all reactions id, reactions ids from reaction file, ratio. sep = "\t"
"""
from padmet.classes import PadmetSpec
from padmet.utils.exploration import get_pwy_from_rxn
import docopt

[docs]def main(): args = docopt.docopt(__doc__) reaction_file = args["--reaction_file"] with open(reaction_file, 'r') as f: reactions = set(f.read().splitlines()) padmet_file = args["--padmetRef"] output = args["--output"] padmet = PadmetSpec(padmet_file) dict_pwy = get_pwy_from_rxn.extract_pwys(padmet, reactions) get_pwy_from_rxn.dict_pwys_to_file(dict_pwy, output)
if __name__ == "__main__": main()