# -*- coding: utf-8 -*-
"""
Description:
#TODO
::
usage:
modelSeed_to_padmet.py --output=FILE --rxn_file=FILE --pwy_file=FILE [-v]
options:
-h --help Show help.
--output=FILE path of the padmet file to create
--rxn_file=FILE path to json file of modelSeed reactions
--pwy_file=FILE path to pathway reactions association from modelSeed
-v print info.
"""
from padmet.node import Node
from padmet.relation import Relation
from padmet.padmetRef import PadmetRef
from datetime import datetime
from time import time
import csv
import json
import docopt
import re
[docs]def main():
global list_of_relation
chronoDepart = time()
#parsing args
args = docopt.docopt(__doc__)
output = args["--output"]
verbose = args["-v"]
rxn_file = args["--rxn_file"]
pwy_file = args["--pwy_file"]
now = datetime.now()
today_date = now.strftime("%Y-%m-%d")
#print(verbose,today_date,version, output, classes_file, compounds_file, proteins_file, reactions_file, enzrxns_file, pathways_file)
policyInArray = [['compound','has_name','name'], ['compound','has_xref','xref'], ['compound','has_suppData','suppData'],
['gene','has_name','name'], ['gene','has_xref','xref'], ['gene','has_suppData','suppData'], ['gene','codes_for','protein'],
['pathway','has_name','name'], ['pathway','has_xref','xref'], ['pathway','is_in_pathway','pathway'],
['protein','has_name','name'], ['protein','has_xref','xref'], ['protein','has_suppData','suppData'], ['protein','catalyses','reaction'],
['reaction','has_name','name'], ['reaction','has_xref','xref'], ['reaction','has_suppData','suppData'], ['reaction','has_reconstructionData','reconstructionData'], ['reaction','is_in_pathway','pathway'],
['reaction','consumes','class','STOICHIOMETRY','X','COMPARTMENT','Y'], ['reaction','produces','class','STOICHIOMETRY','X','COMPARTMENT','Y'],
['reaction','consumes','compound','STOICHIOMETRY','X','COMPARTMENT','Y'], ['reaction','produces','compound','STOICHIOMETRY','X','COMPARTMENT','Y'],
['reaction','consumes','protein','STOICHIOMETRY','X','COMPARTMENT','Y'], ['reaction','produces','protein','STOICHIOMETRY','X','COMPARTMENT','Y'],
['reaction','is_linked_to','gene','SOURCE:ASSIGNMENT','X:Y']]
dbNotes = {"PADMET":{"Creation":today_date, "version":"2.6"}, "DB_info":{"DB":"MODELSEED", "version":"1.0"}}
padmetRef = PadmetRef()
if verbose: print("setting policy")
padmetRef.setPolicy(policyInArray)
if verbose: print("setting dbInfo")
padmetRef.setInfo(dbNotes)
list_of_relation = []
rxn_data = json.load(open(rxn_file))
#remove biomass rxn:
rxn_data.pop("rxn12985")
if verbose: print("updating padmet")
count = 0
for rxn_id, rxn_dict in list(rxn_data.items()):
count += 1
if verbose: print("reaction: %s, %s/%s" %(rxn_id, count, len(rxn_data)))
try:
if not rxn_dict["compound_ids"]:
raise KeyError
except KeyError:
print(rxn_id)
continue
if rxn_id not in list(padmetRef.dicOfNode.keys()):
if rxn_dict["reversibility"] == ">":
rxn_direction = "LEFT-TO-RIGHT"
else:
rxn_direction = "REVERSIBLE"
rxn_name = rxn_dict["name"]
padmetRef.createNode("reaction",rxn_id,{"COMMON_NAME":[rxn_name],"DIRECTION":[rxn_direction]})
rxn_metabolites = rxn_dict["stoichiometry"].split(";")
for metabo_data in rxn_metabolites:
metabo_data = metabo_data.replace("???","\"")
try:
metabo_temp, metabo_name = metabo_data.split("\"")[:2]
metabo_stoich, metabo_id, metabo_compart = metabo_temp.split(":")[:3]
except ValueError:
metabo_stoich, metabo_id, metabo_compart, metabo_name = metabo_data.split(":")[:4]
metabo_stoich = float(metabo_stoich)
#from modelSeed github
if metabo_compart == "0":
metabo_compart = "c"
elif metabo_compart == "1":
metabo_compart = "e"
elif metabo_compart == "2":
metabo_compart = "p"
try:
padmetRef.dicOfNode[metabo_id]
except KeyError:
padmetRef.createNode("compound",metabo_id,{"COMMON_NAME":[metabo_name]})
if metabo_stoich < 0:
consumes_rlt = Relation(rxn_id,"consumes",metabo_id,{"STOICHIOMETRY":[abs(metabo_stoich)],"COMPARTMENT":[metabo_compart]})
list_of_relation.append(consumes_rlt)
else:
produces_rlt = Relation(rxn_id,"produces",metabo_id,{"STOICHIOMETRY":[abs(metabo_stoich)],"COMPARTMENT":[metabo_compart]})
list_of_relation.append(produces_rlt)
else:
if verbose: print("%s already in padmet" %rxn_id)
continue
with open(pwy_file) as csvfile:
reader = csv.DictReader(csvfile, delimiter='\t' )
pwy_raw_data = [row for row in reader]
for pwy_raw in pwy_raw_data:
pwy_id = pwy_raw["Source ID"]
pwy_names = [pwy_raw["Name"],pwy_raw["Aliases"]]
rxn_ids = pwy_raw["Reactions"].split("|")
try:
padmetRef.dicOfNode[pwy_id]
except KeyError:
padmetRef.createNode("pathway",pwy_id,{"COMMON_NAME":pwy_names})
for rxn_id in rxn_ids:
pwy_rlt = Relation(rxn_id,"is_in_pathway",pwy_id)
list_of_relation.append(pwy_rlt)
if verbose: print("Adding all relations")
count = 0
for rlt in list_of_relation:
count += 1
if verbose: print("relation %s/%s" %(count, len(list_of_relation)))
try:
padmetRef.dicOfRelationIn[rlt.id_in].append(rlt)
except KeyError:
padmetRef.dicOfRelationIn[rlt.id_in] = [rlt]
try:
padmetRef.dicOfRelationOut[rlt.id_out].append(rlt)
except KeyError:
padmetRef.dicOfRelationOut[rlt.id_out] = [rlt]
"""
if pwy_file:
add_kegg_pwy(pwy_file, padmetRef, verbose)
"""
if verbose: print("Generating file: %s" %output)
padmetRef.generateFile(output)
chrono = (time() - chronoDepart)
partie_entiere, partie_decimale = str(chrono).split('.')
chrono = ".".join([partie_entiere, partie_decimale[:3]])
if verbose: print("done in: ", chrono, "s !")
[docs]def add_kegg_pwy(pwy_file, padmetRef, verbose = False):
global list_of_relation
with open(pwy_file, 'r') as f:
for data in [line.split("\t") for line in f.read().splitlines()][1:]:
pwy_id, name, ec, rxn_id = data
try:
pwy_node = padmetRef.dicOfNode[pwy_id]
except KeyError:
pwy_node = padmetRef.createNode("pathway", pwy_id)
if name:
try:
pwy_node.misc["COMMON_NAME"].append(name)
except KeyError:
pwy_node.misc["COMMON_NAME"] = [name]
if rxn_id:
if rxn_id in list(padmetRef.dicOfNode.keys()):
pwy_rlt = Relation(rxn_id,"is_in_pathway",pwy_id)
padmetRef._addRelation(pwy_rlt)
else:
if verbose: print("%s in pwy %s but not in padmet" %(rxn_id, pwy_id))
padmetRef.generateFile("/home/maite/Documents/data/bigg/bigg_v2.padmet")
if __name__ == "__main__":
main()