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analyse_all_mn_cpds.py
61 lines (50 loc) · 2.06 KB
/
analyse_all_mn_cpds.py
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import sys
import os
import argparse
import json
from padmet.utils.sbmlPlugin import convert_from_coded_id
from libsbml import SBMLReader, SBMLDocument
"""
Starting from an ontology of compounds into families and a directory of metabolic networks, retrieve for each MN the metabolites it contains and add 1 to each family of these metabolites
"""
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument("-d", "--dir",
help="directory of metabolic networks",
required=True)
parser.add_argument("-j", "--json",
help="json file of family ontologies",
required=True)
parser.add_argument("-o", "--output",
help="output filename for families statistics",
required=True)
args = parser.parse_args()
mn_dir = args.dir
json_family = args.json
outfile = args.output
species_by_mn = {}
for mn in os.listdir(mn_dir):
print(mn)
mn_name = mn.rstrip(".sbml")
reader = SBMLReader()
model = reader.readSBML(mn_dir + '/' + mn).getModel()
species = [convert_from_coded_id(i.getId())[0] for i in model.getListOfSpecies()]
species_by_mn[mn_name] = species
with open(json_family, "r") as f:
family_dict = json.load(f)
# count_dict = {i:0 for i in list(set(sum(family_dict.values(), [])))}
families_by_mn = {}
for mn in species_by_mn:
families_by_mn[mn] = {i:0 for i in list(set(sum(family_dict.values(), [])))}
families_by_mn[mn]["unknown"] = 0
for elem in species_by_mn[mn]:
if elem in family_dict:
for fam in family_dict[elem]:
# count_dict[elem] +=1
families_by_mn[mn][fam] += 1
else:
families_by_mn[mn]["unknown"] += 1
with open(outfile, "w") as g:
for mn in families_by_mn:
for elem in families_by_mn[mn]:
g.write(mn + '\t' + elem + '\t' + str(families_by_mn[mn][elem]) + '\n')