# -*- coding: utf-8 -*-
"""
Description:
Create reports of a padmet file.
all_pathways.tsv: header = ["dbRef_id", "Common name", "Number of reaction found",
"Total number of reaction", "Ratio (Reaction found / Total)"]
all_reactions.tsv: header = ["dbRef_id", "Common name", "formula (with id)",
"formula (with common name)", "in pathways", "associated genes"]
all_metabolites.tsv: header = ["dbRef_id", "Common name", "Produced (p), Consumed (c), Both (cp)"]
::
usage:
padmet report_network --padmetSpec=FILE --output_dir=dir [--padmetRef=FILE] [-v]
options:
-h --help Show help.
--padmetSpec=FILE pathname of the padmet file.
--padmetRef=FILE pathname of the padmet file used as database
--output_dir=dir directory for the results.
-v print info.
"""
import docopt
from padmet.classes import PadmetSpec
[docs]
def command_help():
"""
Show help for analysis command.
"""
print(docopt.docopt(__doc__))
[docs]
def report_network_cli(command_args):
args = docopt.docopt(__doc__, argv=command_args)
padmetRef_file = args["--padmetRef"]
padmetSpec = PadmetSpec(args["--padmetSpec"])
output_dir = args["--output_dir"]
verbose = args["-v"]
padmetSpec.network_report(output_dir, padmetRef_file, verbose)