convertModel.py

# converts reaction list and descrition in a text file to GAMS input format
__author__      = "Mohammad Mazharul Islam and Wheaton Schroeder"
#version 1.0: Mohammad
#version 1.1: Wheaton
#updates associated with version 1.1:
#*updated the output to write all files necessary for fba.gms (added exchange_reactions.txt'
#	irreversible_reactions.txt, and reversible_reactions_no_exchange such that this programs
#	output is the input to fba.gms.
#	This program is dependent on the nomenclature in kathKeys.txt, and was originally written
#	to streamline the time to FBA using personal notation
#*minor streamlining of some lines of code, variable addition associated with previous bullet update
#*added command line output so that the user knows the program ran successfully

#importing the string package
import string
#import the regular expression package
import re

#this is the input file, 'r' denotes read operation
input1=open('Model.txt','r')

#these are the output file names, 'w' denotes write operation
output1=open('mets.txt','w')
output2=open('rxntype.txt','w')
output3=open('Sij.txt','w')
output4=open('rxns.txt','w')
output5=open('ex_rxns.txt','w')
output6=open('irrev_rxns_f.txt','w')
output7=open('rev_rxns_no_ex.txt','w')
output8=open('reg_rxns.txt','w')
output9=open('irrev_rxns_b.txt','w')
output10=open('medium.txt','w')


#reading the input file
alllines1=input1.readlines()

#declaring empty lists for metabolites and reactions (where each metabolite and reaction will be added one by one after reading the input file)
#complete metabolite list
met_list=[]
#complete reaction list
rxn_list=[]
#list of irreversible reactions
irr_rxn_list=[]
#list of reactions that are reversible, but not exchange
rev_rxn_no_ex_list=[]
#list of exchange reactions
ex_rxn_list=[]
#list of regulated reactions
reg_rxn_list=[]
#list of sink reactions
sink_rxn_list=[]
#objective species
objective=""

output1.write('/\n') #writing a '/' mark at the beginning of the output file 1, then new line (metabolites.txt)
output2.write('/\n') #writing a '/' mark at the beginning of the output file 2, then new line (rxntype.txt)
output3.write('/\n') #writing a '/' mark at the beginning of the output file 3, then new line (S_matrix.txt)
output4.write('/\n') #writing a '/' mark at the beginning of the output file 4, then new line (reactions.txt)
output5.write('/\n') #writing a '/' mark at the beginning of the output file 5, then new line (exchange_reactions.txt)
output6.write('/\n') #writing a '/' mark at the beginning of the output file 6, then new line (irreversible_reactions_f.txt)
output7.write('/\n') #writing a '/' mark at the beginning of the output file 7, then new line (reversible_reactions_no_exchange.txt)
output8.write('/\n') #writing a '/' mark at the beginning of the output file 8, then new line (regulated_reactions.txt)
output9.write('/\n') #writing a '/' mark at the beginning of the output file 8, then new line (regulated_reactions_b.txt)
output10.write('/\n') #writing a '/' mark at the beginning of the output file 8, then new line (regulated_reactions_b.txt)

for line in alllines1:	#for each line in the input file
	
	#this should allow comments lines that are deliniated by # at the start off the line
	if bool(re.search('^#',line)):
		
		#ignore this line, this line is a comment
		print('comment line: \"'+line+'\"')
	
	else:
	
		line=line.rstrip()	# stripping off any empty characters at the end of the line
		rxn,des=line.split('\t')	#splitting the remaining line with a tab separator, in this case rxn will give reaction name, and des will give you the rest
		print(rxn)
		#Quick key:
		#rxn - reaction name/number/id/etc
		#des - reaction descrition, the written out chemical reaction, possibly with stoichiometry
		
		#block of text to handle regulated reactions before going into if/else scenarios
		if bool(re.search('reg$',rxn)):	#if has reg tag, note that regular expression search converted to boolean 
			if rxn not in reg_rxn_list:	#if not already it regulated reactions list
				reg_rxn_list.append(rxn)	#append it to list
				output8.write("'"+rxn+"'\n")	#write it to appropriate file
		
		if '->' in line and '<->' not in line:	#if a forward reaction	
			reactant=des.split('->')[0] #splitting the "des" at '->' sign, [0] gives the first portion
			product=des.split('->')[1] #[1] gives the second
			dir='->'	#directionality
			state='1'
			#find out if objective function, save objective species
			if bool(re.search("biomass_ch",rxn)):
				objective=reactant
			if rxn not in irr_rxn_list:
				irr_rxn_list.append(rxn)	#add this reaction to irreversible list
				output6.write("'"+rxn+"'\n")	#writes reaction to irreversible reaction list
					#find out if exchange or not
			if bool(re.search('ex$',rxn)):	#if exchange reaction, not that it is converted to a boolean of a regular expression search
				if rxn not in ex_rxn_list:
					ex_rxn_list.append(rxn)	#add to exchange reaction list
					output5.write("'"+rxn+"'\n") #write reaction to exchange reaction list
			if bool(re.search('si$',rxn)):
				if rxn not in sink_rxn_list:
					sink_rxn_list.append(rxn)
		elif '<-' in line and '<->' not in line:	#if a reverse reaction
			reactant=des.split('<-')[0]
			product=des.split('<-')[1]
			dir='<-'	#directionality
			state='-1'
			if rxn not in irr_rxn_list:
				irr_rxn_list.append(rxn)	#add this reaction to irreversible list
				output9.write("'"+rxn+"'\n")	#writes reaction to irreversible reaction list
					#find out if exchange or not
			if bool(re.search('ex$',rxn)):	#if exchange reaction, not that it is converted to a boolean of a regular expression search
				if rxn not in ex_rxn_list:
					ex_rxn_list.append(rxn)	#add to exchange reaction list
					output5.write("'"+rxn+"'\n") #write reaction to exchange reaction list
					output10.write("'"+rxn+"'\n") #write reaction to exchange reaction list
			if bool(re.search('si$',rxn)): #find out if sink reaction
				if rxn not in sink_rxn_list:
					sink_rxn_list.append(rxn)
		else:	#if a reversible reaction
			reactant=des.split('<->')[0]
			product=des.split('<->')[1]
			dir='<->'	#directionality
			state='0'
			#find out if exchange or not
			if bool(re.search('ex$',rxn)):	#if exchange reaction, not that it is converted to a boolean of a regular expression search
				if rxn not in ex_rxn_list:
					ex_rxn_list.append(rxn)	#add to exchange reaction list
					output5.write("'"+rxn+"'\n") #write reaction to exchange reaction list
					output10.write("'"+rxn+"'\n") #write reaction to exchange reaction list
			else:	#otherwise, it is not an exchange reaction
				if rxn not in rev_rxn_no_ex_list:
					rev_rxn_no_ex_list.append(rxn)	#append reversible but not exchange list
					output7.write("'"+rxn+"'\n")	#writes reaction to list of reversible reactions that are not exchange reactions
			if bool(re.search('si$',rxn)): #find out if sink reaction
				if rxn not in sink_rxn_list:
					sink_rxn_list.append(rxn)
		if rxn not in rxn_list:
			rxn_list.append(rxn) 	#if the reaction name was not already in the reaction list, we are adding it
			output2.write( "'"+ rxn + "' " + state)	#writing the output in the rxntype.txt file
			output2.write('\n')	#newline
			output4.write("'"+ rxn + "'")
			output4.write('\n')	#newline
				
		dummy_list=reactant.split(' + ') #splitting the reactant side and getting the individual reactants
		k=0
		while k<len(dummy_list): #for every reactant, splitting the stochiometric coefficients
			ind_react=dummy_list[k]
			ind_react=ind_react.strip()
			if ' ' in ind_react:
				st, react_compt = ind_react.split()
			else:
				st = 1
				react_compt = ind_react
				
			if react_compt not in met_list:
				met_list.append(react_compt)  	#if the metabolite name was not already in the metabolite list, we are adding it
				output1.write("'"+react_compt+ "'")
				output1.write('\n')	#newline
			#joining the reactant name and rxn name and stoichiometric coefficinet to write into output3 (Sij.txt)
			stoich_line = "'" + react_compt + "'" +'.'+"'" + rxn +"'" +'  '+'-'+str(st)
			output3.write(stoich_line)
			output3.write('\n')	#newline
					
			k=k+1
				
				
		if product != '':
				
			dummy_list2=product.split(' + ') #splitting the product side and getting the individual products
					
			kk=0
			while kk<len(dummy_list2):  #for every product, splitting the stochiometric coefficients
				ind_prod=dummy_list2[kk]
				ind_prod=ind_prod.strip()
				if ' ' in ind_prod:
					st,prod_compt=ind_prod.split()
				else:
					st = 1
					prod_compt = ind_prod
				
				if prod_compt not in met_list:
					met_list.append(prod_compt)
					output1.write("'"+prod_compt+"'")
					output1.write('\n')	#newline

				# joining the product name and rsn name and stoichiometric coefficinet to write into output3 (Sij.txt)
				stoich_line = "'" + prod_compt+ "'" +'.'+"'" +rxn+"'" +'  '+str(st)
				output3.write(stoich_line)
				output3.write('\n')	#newline
					
				kk=kk+1
			
		
	

#add the ending '/' mark to note the end of the file
output1.write('/')
output2.write('/')
output3.write('/')
output4.write('/')
output5.write('/')
output6.write('/')
output7.write('/')
output8.write('/')
output9.write('/')
output10.write('/')

#outputs to let the user know the stats, and show that something has happened
print("number metabolites: "+str(len(met_list))) 	#printing the total number of metabolites
print("number reactions: "+str(len(rxn_list)))	#printing the total number of reactions
print("irreversible reactions: "+str(len(irr_rxn_list))) #print number of irreversible reactions
print("exchange reactions: "+str(len(ex_rxn_list)))	#print number of exchange reactions
print("sink reactions: "+str(len(sink_rxn_list)))	#print number of exchange reactions
print("objective: "+objective)	#print ojective