/
convert_to_SBML.py
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/
convert_to_SBML.py
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"""
Converts pathways under json format to SBML format
"""
# General utilities
import sys
import logging
import csv
import copy
import json
import pickle
import libsbml
from hashlib import md5
import os
import argparse
# RP3 specific objects
from compound import Compound
from move import Move
def _nameToSbmlId(name):
IdStream = []
count = 0
end = len(name)
if '0' <= name[count] and name[count] <= '9':
IdStream.append('_')
for count in range(0, end):
if (('0' <= name[count] and name[count] <= '9') or
('a' <= name[count] and name[count] <= 'z') or
('A' <= name[count] and name[count] <= 'Z')):
IdStream.append(name[count])
else:
IdStream.append('_')
Id = ''.join(IdStream)
if Id[len(Id) - 1] != '_':
return Id
return Id[:-1]
def add_specy(sbml_model,
chemId = 'Id_cmpound',
smiles = "smilescomppoun",
inchi = "inchicompounds",
inchiKey = "inchiKeycomppoun",
name = "compounds_name",
in_sink = False):
spe = sbml_model.createSpecies()
spe.setCompartment("cytoplasm")
spe.setHasOnlySubstanceUnits(False)
spe.setBoundaryCondition(False)
spe.setConstant(False)
spe.setInitialConcentration(1.0)
clean_id = str(chemId)+'__64__'+str("cytoplasm")
clean_id = clean_id.replace('-', '_') # No - in name
metaid = _nameToSbmlId(md5(str(name).encode('utf-8')).hexdigest())
spe.setMetaId(metaid)
spe.setName(name)
if in_sink:
annotation = '''<annotation>
<rdf:RDF
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">'''
annotation += '''
<rdf:RP3 rdf:about="#'''+str(metaid or '')+'''">
<RP3:RP3 xmlns:RP3="https://github.com/brsynth">
<RP3:smiles>'''+str(smiles or '')+'''</RP3:smiles>
<RP3:inchi>'''+str(inchi or '')+'''</RP3:inchi>
<RP3:inchikey>'''+str(inchiKey or '')+'''</RP3:inchikey>
<RP3:in_sink>'''+ str(True)+'''</RP3:in_sink>
</RP3:RP3>
</rdf:RP3>'''
annotation += '''
</rdf:RDF>
</annotation>'''
else:
annotation = '''<annotation>
<rdf:RDF
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">'''
annotation += '''
<rdf:RP3 rdf:about="#'''+str(metaid or '')+'''">
<RP3:RP3 xmlns:RP3="https://github.com/brsynth">
<RP3:smiles>'''+str(smiles or '')+'''</RP3:smiles>
<RP3:inchi>'''+str(inchi or '')+'''</RP3:inchi>
<RP3:inchikey>'''+str(inchiKey or '')+'''</RP3:inchikey>
</RP3:RP3>
</rdf:RP3>'''
annotation += '''
</rdf:RDF>
</annotation>'''
spe.setAnnotation(annotation)
return(sbml_model)
def add_reaction(sbml_model,
reacId = 'Id_reac',
ec = "Test_ec",
rule_id = "rule_id",
biological_score = "biological_score",
chemical_score = "chemical_score",
reactant_stoechio = {},
product = "product_name",
reaction_smiles = "reaction_smiles",
diameter = "diameter"):
reac = sbml_model.createReaction()
reac_fbc = reac.getPlugin('fbc')
reac_fbc.setUpperFluxBound('B_999999')
reac_fbc.setLowerFluxBound('B_0')
#reactions
reac.setId(reacId)
reac.setSBOTerm(185)
reac.setReversible(True)
reac.setFast(False)
metaid = _nameToSbmlId(md5(str(reacId).encode('utf-8')).hexdigest())
reac.setMetaId(metaid)
#reactants_dict
for reactant in reactant_stoechio.keys():
chemId = reactant
spe = reac.createReactant()
clean_id = str(chemId)+'__64__'+str("cytoplasm")
clean_id = clean_id.replace('-', '_') # No - in name
spe.setSpecies(clean_id)
spe.setConstant(True)
try:
stoechio = reactant_stoechio[reactant]
except KeyError:
stoechio = 1
spe.setStoichiometry(stoechio)
#products_dict
if not product is None:
pro = reac.createProduct()
clean_id = str(product)+'__64__'+str("cytoplasm")
clean_id = clean_id.replace('-', '_') # No - in name
pro.setSpecies(clean_id)
pro.setConstant(True)
pro.setStoichiometry(1)
#annotation
annotation = '''<annotation>
<rdf:RDF
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">'''
annotation += '''
<rdf:RP3 rdf:about="#'''+str(metaid or '')+'''">
<RP3:RP3 xmlns:RP3="https://github.com/brsynth">
<RP3:smiles>'''+str(reaction_smiles or '')+'''</RP3:smiles>
<RP3:rule_id>'''+str(rule_id or '')+'''</RP3:rule_id>
<RP3:EC>'''+str(ec)+'''</RP3:EC>
<RP3:biological_score value="'''+str(biological_score or '')+'''" />
<RP3:chemical_score value="'''+str(chemical_score or '')+'''" />
<RP3:diameter value="'''+str(diameter or '')+'''" />
</RP3:RP3>
</rdf:RP3>
</rdf:RDF>
</annotation>'''
reac.setAnnotation(annotation)
return(sbml_model)
def convert_json_to_SBML(json_file, modelID = "test", folder_to_save = 'temp'):
# Set up the empty model
smbl_namespace = libsbml.SBMLNamespaces(3,1)
smbl_namespace.addPkgNamespace('fbc',2)
smbl_namespace.addPkgNamespace('groups',2)
document = libsbml.SBMLDocument(smbl_namespace)
sbml_model = document.createModel()
sbml_model.getPlugin('fbc')
sbml_model.getPlugin('groups')
sbml_model.setId(modelID)
sbml_model.setName(modelID)
sbml_model.setTimeUnits('second')
sbml_model.setExtentUnits('mole')
sbml_model.setSubstanceUnits('mole')
# Could implement units, currently removed from the model
# Should have it in a seperate function
compartment = sbml_model.createCompartment()
compartment.setId("cytoplasm")
target_node = None
for node in json_file["elements"]["nodes"]:
if node["data"]["type"] == "compound":
sbml_model = add_specy(sbml_model,
chemId = node["data"]["id"],
smiles = node["data"]["SMILES"],
inchi = node["data"]["InChI"],
inchiKey = node["data"]["id"],
name = ",".join(node["data"]["Names"]),
in_sink = node["data"]["inSink"] == 1)
if node["data"]["isSource"] == 1:
logging.info("Target node is {}".format(node["data"]["id"]))
target_node = node
for element in sbml_model.getListOfSpecies():
logging.debug(element)
for node in json_file["elements"]["nodes"]:
if node["data"]["type"] == "reaction":
try:
reactant_stoechio = node["data"]["Stoechiometry"]
except KeyError:
reactant_stoechio = {}
sbml_model = add_reaction(sbml_model,
reacId = node["data"]["id"],
ec = ','.join(node["data"]["EC number"]),
rule_id = ','.join(node["data"]["Rule ID"]),
biological_score = node["data"]["Score"],
chemical_score = node["data"]["ChemicalScore"],
reactant_stoechio = reactant_stoechio,
product = node["data"]["id"].split("-RR")[0],
reaction_smiles = node["data"]["Reaction SMILES"],
diameter = node["data"]["Diameter"])
sbml_model = add_reaction(sbml_model,
reacId = "production",
ec = 'NA',
rule_id = 'NA',
biological_score = 'NA',
chemical_score = 'NA',
reactant_stoechio = {target_node["data"]["id"]: 1},
product = None,
reaction_smiles = 'NA',
diameter = 'NA')
document.setModel(sbml_model)
libsbml.writeSBMLToFile(document,'{}/{}.xml'.format(folder_to_save, modelID))
pass
def __cli():
def define_folder_to_save(folder):
if folder is None:
folder_to_save = os.path.join('debugging_results', args.c_name)
else:
folder_to_save = folder
if not os.path.exists(folder_to_save):
os.makedirs(folder_to_save, exist_ok=True)
return folder_to_save
d = "Command line interface to convert json files to SBML files"
parser = argparse.ArgumentParser(description=d)
# Logs and saving information
"""Command line interface to convert json files to SBML files"""
parser.add_argument("--verbose", help="Default logger is INFO, switch to DEBUG is specified",
dest='verbose', action='store_true', default=False)
parser.add_argument("--log_file", help="Default logger is stderr, switch to log_file if specified",
default=None)
parser.add_argument("--folder_to_save",
help="Folder to store results. Default: temp",
default="temp")
parser.add_argument("--json_convert",
help="File to convert",
default="deoxi_07_no_H/deoxiviolacein_iteration_85.json")
parser.add_argument("--file_name", help = 'File name if name changes.', default = None)
args = parser.parse_args()
# Setting up the logs
if args.verbose:
logging_level = logging.DEBUG
else:
logging_level = logging.INFO
if args.log_file is None:
logging.basicConfig(stream=sys.stderr,
level=logging_level,
datefmt='%d/%m/%Y %H:%M:%S',
format='%(asctime)s -- %(levelname)s -- %(message)s')
else:
if not "log" in args.log_file:
log_file = "log_" + args.log_file
else:
log_file = args.log_file
log_writer = open("{}/{}".format(folder_to_save, log_file), "w")
logging.basicConfig(stream=log_writer,
level=logging_level,
datefmt='%d/%m/%Y %H:%M:%S',
format='%(asctime)s -- %(levelname)s -- %(message)s')
folder_to_save = define_folder_to_save(args.folder_to_save)
# Choosing file
if args.file_name is None:
model_ID = args.json_convert.split("/")[-1].split(".json")[0]
else:
model_ID = args.file_name
pathway_to_test = json.load(open(args.json_convert, "r"))
convert_json_to_SBML(pathway_to_test, model_ID, folder_to_save = folder_to_save)
if __name__ == "__main__":
__cli()