# -*- coding: utf-8 -*-
"""
Description:
For a given set of compounds representing the growth medium (or seeds). Create 2 reactions
for each compounds to maintain consistency of the network for flux analysis.
For each compounds create:
An exchange reaction: this reaction consumes the compound in the
compartment 'C-BOUNDARY' and produces the compound in the compartment 'e' extracellular
A transport reaction: this reaction consumes the compound in the compartment
'e' extracellular' and produces the compound in the compartment 'c' cytosol
ex: for seed 'cpd-a'
1/ check if cpd-a in padmetSpec, if not, copy from padmetRef.
2/ create exchange reaction: ExchangeSeed_cpd-a_b: 1 cpd-a (C-BOUNDARAY) <=> 1 cpd-a (e)
3/ create transport reaction: TransportSeed_cpd-a_e: 1 cpd-a (e) => 1 cpd-a (c)
4/ create a new file if output not None, or overwrite padmetSpec
::
usage:
padmet_medium.py --padmetSpec=FILE
padmet_medium.py --padmetSpec=FILE -r [--output=FILE] [-v]
padmet_medium.py --padmetSpec=FILE --seeds=FILE [--padmetRef=FILE] [--output=FILE] [-v]
options:
-h --help Show help.
--padmetSpec=FILE path to the padmet file to update
--padmetRef=FILE path to the padmet file representing to the database of reference (ex: metacyc_18.5.padmet)
--seeds=FILE the path to the file containing the compounds ids and the compart, line = cpd-id\tcompart.
--output=FILE If not None, pathname to the padmet file updated
-r Use to remove all medium from padmet
-v print info
"""
import docopt
from padmet.classes import PadmetSpec
from padmet.classes import PadmetRef
[docs]def main():
args = docopt.docopt(__doc__)
if args["--seeds"]:
with open(args["--seeds"], 'r') as f:
seeds = [line.split("\t")[0] for line in f.read().splitlines()]
else:
seeds = None
padmet = PadmetSpec(args["--padmetSpec"])
if args["--padmetRef"]:
padmetRef = PadmetRef(args["--padmetRef"])
else:
padmetRef = None
output = args["--output"]
verbose = args["-v"]
remove = args["-r"]
if output is None:
output = args["--padmetSpec"]
if not remove and not seeds:
g_m = padmet.get_growth_medium()
print("List of growth medium:")
if g_m:
print(list(g_m))
else:
print("[]")
else:
manage_medium(padmet, seeds, padmetRef, verbose)
padmet.generateFile(output)
[docs]def manage_medium(padmet, new_growth_medium=None, padmetRef=None, verbose=False):
"""
Manage medium of a padmet. If new_growth_medium give, use this list of compound
to define the new medium and create transport and exchange reactions.
if padmetRef given, use the information from padmetRef to create the missing compound.
If no new_growth_medium given: remove the current medium in the padmet.
Parameters
----------
padmet: padmet.classes.PadmetSpec
padmet to update
new_growth_medium: list
list of compound id representing the medium
padmetRef: padmet.classes.PadmetRef
padmet containing the database of reference
verbose: bool
if True print information
Returns
-------
padmet.classes.PadmetSpec:
New padmet after updating medium
"""
if new_growth_medium:
padmet.set_growth_medium(new_growth_medium=new_growth_medium, padmetRef=padmetRef, verbose=verbose)
else:
padmet.remove_growth_medium(verbose=verbose)
return padmet
if __name__ == "__main__":
main()