# -*- coding: utf-8 -*-
"""
Description:
For a given padmet file, check and update compartment.
1./ Get all compartment with 1st usage
2./ Remove a compartment with 2nd usage.
Remove all reactions acting in the given compartment
3./ change compartment id with 3rd usage
::
usage:
padmet_compart.py --padmet=FILE
padmet_compart.py --padmet=FILE --remove=STR [--output=FILE] [-v]
padmet_compart.py --padmet=FILE --old=STR --new=STR [--output=FILE] [-v]
options:
-h --help Show help.
--padmet=FILE pathname of the padmet file
--remove=STR compartment id to remove
--old=STR compartment id to change to new id
--new=STR new compartment id
--output=FILE new padmet pathname, if none, overwritting the original padmet
-v print info
"""
from padmet.classes import PadmetSpec
import docopt
__all__ = ["remove_compart", "remplace_compart"]
def main():
#parsing args
args = docopt.docopt(__doc__)
padmet_file = args["--padmet"]
old_compart = args["--old"]
new_compart = args["--new"]
new_padmet = args["--output"]
to_remove = args["--remove"]
verbose = args["-v"]
if new_padmet is None:
new_padmet = args["--padmet"]
padmet = PadmetSpec(padmet_file)
if to_remove:
padmet = remove_compart(padmet, to_remove, verbose = False)
padmet.generateFile(new_padmet)
elif old_compart and new_compart:
padmet = remplace_compart(padmet, old_compart, new_compart, verbose)
padmet.generateFile(new_padmet)
else:
print("List of compartments:")
print(list(padmet.get_all_compart()))
[docs]def remove_compart(padmet, to_remove, verbose = False):
"""
Remove all reaction associated to a compound in the compartment to remove.
Parameters
----------
padmet: padmet.classes.PadmetSpec
padmet to udpate
to_remove: str
compartment id to remove, if many separate compartment id by ','
verbose: bool
if True print information
Returns
-------
padmet.classes.PadmetSpec:
New padmet after removing compartment(s)
"""
if "," in to_remove:
to_remove = to_remove.split(",")
else:
to_remove = [to_remove]
for compart in to_remove:
if verbose:
print("removing reaction(s) in compartment %s" %compart)
padmet.delCompart(compart, verbose)
return padmet
[docs]def remplace_compart(padmet, old_compart, new_compart, verbose = False):
"""
Remplace compartment 'old_compart' by 'new_compart'.
Parameters
----------
padmet: padmet.classes.PadmetSpec
padmet to udpate
old_comaprt: str
compartment id to remplace
new_compart: str
new compartment id
verbose: bool
if True print information
Returns
-------
padmet.classes.PadmetSpec:
New padmet after remplacing compartment
"""
if verbose:
print("Converting compartment %s to %s" %(old_compart, new_compart))
padmet.change_compart(old_compart, new_compart, verbose)
return padmet
if __name__ == "__main__":
main()