#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Description:
Convert PADMet to ASP following these predicats:
common_name({reaction_id or enzyme_id or pathway_id or compound_id} , common_name)
direction(reaction_id, reaction_direction). reaction_direction in[LEFT-TO-RIGHT,REVERSIBLE]
ec_number(reaction_id, ec(x,x,x)).
catalysed_by(reaction_id, enzyme_id).
uniprotID(enzyme_id, uniprot_id). #if has has_xref and db = "UNIPROT"
in_pathway(reaction_id, pathway_id).
reactant(reaction_id, compound_id, stoechio_value).
product(reaction_id, compound_id, stoechio_value).
is_a(compound_id, class_id).
is_a(pathway_id, pathway_id).
::
usage:
padmet_to_asp.py --padmet=FILE --output=FILE [-v]
option:
-h --help Show help.
--padmet=FILE path to padmet file to convert.
--output=FILE path to output file in lp format.
-v print info.
"""
from padmet.utils.connection import padmet_to_asp
import docopt
[docs]def main():
args = docopt.docopt(__doc__)
padmet_file = args["--padmet"]
output = args["--output"]
verbose = args["-v"]
padmet_to_asp.padmet_to_asp(padmet_file, output, verbose)
if __name__ == "__main__":
main()