Source code for padmet_utils.connection.sbml_to_curation_form

# -*- coding: utf-8 -*-
    extract 1 reaction (if rxn_id) or a list of reactions (if rxn_file) 
    from a sbml file to the form used in aureme for curation.
    For example use this script to extract specific missing reaction of a model to
    a just created metabolic network.


    usage: --sbml=FILE --output=FILE --rxn_id=ID [--comment=STR] [--extract-gene] [-v] --sbml=FILE --output=FILE --rxn_file=FILE [--comment=STR] [--extract-gene] [-v]
        -h --help     Show help.
        --sbml=FILE    path of the sbml.
        --output=FILE    form containing the reaction extracted, form used for manual curation in aureme.
        --rxn_id=FILE    id of one reaction to extract
        --rxn_file=FILE    file of reactions ids to extract, 1 id by line.
        --extract-gene    If true, extract also genes associated to reactions.
        --comment=STR    comment associated to the reactions in the form. Used to track sources of curation in aureme [default: "N.A"].
        -v   print info


import docopt
from padmet.utils.connection import sbml_to_curation_form

[docs]def main(): args = docopt.docopt(__doc__) sbml_file = args["--sbml"] if args["--rxn_id"]: rxn_list = [args["--rxn_id"]] if args["--rxn_file"]: with open(args["--rxn_id"], 'r') as f: rxn_list = output = args["--output"] comment = args["--comment"] verbose = args["-v"] extract_gene = args["--extract-gene"] sbml_to_curation_form.sbml_to_curation(sbml_file, rxn_list, output, extract_gene=extract_gene, comment=comment, verbose=verbose)
if __name__ == "__main__": main()