cdanielmachado / kefir_paper Goto Github PK

import sys
import glob
import cobra
import reframed
from reframed import load_cbmodel
from reframed import Environment
from reframed import FBA

# Loop to read in models in hardcoded folder with .xml extension
for file in glob.iglob(r'*.xml'):
	
	# Use try to handle exceptions with reading SMBL model
	try:

		# Load model
		model = load_cbmodel(file, flavor='cobra')

		# SIM 1: Use Milk media env
		env = Environment.from_compounds(["h2o","o2","co2","ca2","cl","cobalt2","cu2","fe2","fe3","h","k","mg2","mn2","mobd","na1","nh4","ni2","pi","so4","zn2","ala__L","asn__L","asp__L","glu__L","gln__L","gly","his__L","ile__L","leu__L","lys__L","orn","phe__L","peamn","pro__L","ser__L","thr__L","trp__L","tyr__L","val__L","lcts","glc__D","gal","gal_bD","cit","lac__D","lac__L","for","ac","oxa","pydx","cbl1","thm","pnto__R","fol","ribflv","nac","btn","but","caproic","octa","dca","ddca","ttdca","ptdca","hdca","ocdca","arach","ttdcea","hdcea","ocdcea","lnlc","arachd","ade","gua","ins","thymd","ura","xan","4abut"])

		# SIM 1: Solve FBA
		sol = FBA(model, constraints=env)

		# SIM 1: Open text file with .exf (exchange fluxes) extension
		sys.stdout = open(file+"_milk.exf", "w")

		# SIM 1: Get exchange fluxes
		exf = sol.show_values(pattern="R_EX", sort=True)

		# SIM 2: Constrain uptake of nutrients not in milk media
		model.reactions.R_EX_glyald_e.lb = 0
		model.reactions.R_EX_glyc3p_e.lb = 0
		model.reactions.R_EX_gthrd_e.lb = 0
		model.reactions.R_EX_h2o2_e.lb = 0
		model.reactions.R_EX_acald_e.lb = 0
		model.reactions.R_EX_ala__D_e.lb = 0
		model.reactions.R_EX_mal__L_e.lb = 0
		#model.reactions.R_EX_2pglyc_e.lb = 0

		# SIM 2: Run FBA
		sol = FBA(model)

		# SIM 2: Open text file with .exf (exchange fluxes) extension
		sys.stdout = open(file+"_milkm.exf", "w")

		# SIM 2: Get exchange fluxes
		exf = sol.show_values(pattern="R_EX", sort=True)

	# Catch cobra.io.sbml.CobraSBMLError and continue loop    
	except cobra.io.sbml.CobraSBMLError:

		# Print message with model ID for log
		print("The model",file,"raised an SBML error and could not be read in by COBRA")

		#Nothing to see here fellas
		pass