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get_shadow_prices.py
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#! /usr/bin/python
#! python3.7
#try to specify that will use python version 3.7
__author__ = "Wheaton Schroeder"
#This code is created to read the gams-based input files for a genome scale model and instead create a GSM using the
#cobrapy tool. This is then followed by performing flux balance analysis (FBA) on the given model
#This was written to satisfy the request of reviewers for the protocol paper:
#Optfill, Shadow Price, and the Genome-Scale Exophiala dermatitidis Reconstruction iEde2091: Procedure and Application
#as a Model of Pigment Synthesis
#By: Wheaton L Schroeder and Rajib Saha
#Submitted to STAR Protocols
#latest version: 06/17/2020
#run the model convert files
import os
import cobra
#from cobra import Model, Reaction, Metabolite
from cobra import Model, Reaction, Metabolite
#read the model with cobrapy
model = cobra.io.read_sbml_model("iEde2091.xml")
#output file, report things like reaction rates
output=open('shadow_price_python_output.tsv','w')
#need to write the header for shadow costs
output.write("Trial#\tcode\tgrowth\tX00001[c]\tC04033[c]\tC00779[c]\tC01173[c]\tC01624[c]\tC00083[c]\tC17937DHN[e]\t")
output.write("C05578[e]\tC05579[e]\tC01693[e]\tC05604[e]\tC00355[c]\tC00822[c]\tC00082[c]\tC17937Eu[e]\tC00544[c]\t")
output.write("X00002[c]\tC01179[c]\tC17937Pyo[e]\tC00353[c]\tC03427[c]\tC05421[c]\tC05414[c]\tC05430[c]\tC05431[c]\t")
output.write("C05432[c]\tC05435[c]\tC15867[c]\tC08613[c]\tC02094[c]\tC19892[c]\tC08607[c]\tC00097[c]\tModel Status\n")
#specify the bounds
M = 10000 #positive really big number (arbitrary)
#track trial number
trial = 1;
########################################## TRIAL 1 ##########################################
# Carbon-limited sucrose as carbon source, LB(R003ex) = -0.25 #
#############################################################################################
#set the bounds for exchange reactions
#note that ".lowerbound" does not appear to work, only ".lower_bound"
#note that ".upperbound" does not appear to work, only ".upper_bound"
model.reactions.get_by_id("R001ex").lower_bound = -M #water
model.reactions.get_by_id("R002ex").lower_bound = -M #phosphate
model.reactions.get_by_id("R003ex").lower_bound = -0.25 #sucrose
model.reactions.get_by_id("R004ex").lower_bound = -M #ammonia
model.reactions.get_by_id("R005ex").lower_bound = -M #sulfate
model.reactions.get_by_id("R006ex").lower_bound = -M #protons
model.reactions.get_by_id("R007ex").lower_bound = 0 #carbon dioxide
model.reactions.get_by_id("R008ex").lower_bound = -M #oxygen
model.reactions.get_by_id("R009ex").lower_bound = 0 #ethanol
model.reactions.get_by_id("R010ex").lower_bound = 0 #acetate
model.reactions.get_by_id("R011ex").lower_bound = 0 #glucose
model.reactions.get_by_id("R012ex").lower_bound = 0 #urate
model.reactions.get_by_id("R001ex").upper_bound = M #water
model.reactions.get_by_id("R002ex").upper_bound = 0 #phosphate
model.reactions.get_by_id("R003ex").upper_bound = 0 #sucrose
model.reactions.get_by_id("R004ex").upper_bound = 0 #ammonia
model.reactions.get_by_id("R005ex").upper_bound = 0 #sulfate
model.reactions.get_by_id("R006ex").upper_bound = M #protons
model.reactions.get_by_id("R007ex").upper_bound = M #carbon dioxide
model.reactions.get_by_id("R008ex").upper_bound = 0 #oxygen
model.reactions.get_by_id("R009ex").upper_bound = M #ethanol
model.reactions.get_by_id("R010ex").upper_bound = 0 #acetate
model.reactions.get_by_id("R011ex").upper_bound = 0 #glucose
model.reactions.get_by_id("R012ex").upper_bound = M #urate
model.repair()
#solve FBA
solution = model.optimize()
#need to write the shadow prices
output.write(str(trial)+"\t")
output.write(str("SCL\t"))
output.write("{:e}".format(solution.objective_value)+"\t")
output.write("{:e}".format(solution.shadow_prices.X00001__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C04033__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00779__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01173__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01624__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00083__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C17937DHN__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05578__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05579__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01693__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05604__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00355__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00822__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00082__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C17937Eu__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00544__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.X00002__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01179__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C17937Pyo__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00353__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C03427__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05421__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05414__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05430__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05431__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05432__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05435__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C15867__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C08613__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C02094__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C19892__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C08607__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00097__c)+"\t")
output.write("1\n")
trial=trial+1
print("Trial "+str(trial)+" running...\n")
########################################## TRIAL 2 ##########################################
# Carbon-limited sucrose as carbon source, LB(R003ex) = -0.50 #
#############################################################################################
#set the bounds for exchange reactions
#note that ".lowerbound" does not appear to work, only ".lower_bound"
#note that ".upperbound" does not appear to work, only ".upper_bound"
model.reactions.get_by_id("R001ex").lower_bound = -M #water
model.reactions.get_by_id("R002ex").lower_bound = -M #phosphate
model.reactions.get_by_id("R003ex").lower_bound = -0.50 #sucrose
model.reactions.get_by_id("R004ex").lower_bound = -M #ammonia
model.reactions.get_by_id("R005ex").lower_bound = -M #sulfate
model.reactions.get_by_id("R006ex").lower_bound = -M #protons
model.reactions.get_by_id("R007ex").lower_bound = 0 #carbon dioxide
model.reactions.get_by_id("R008ex").lower_bound = -M #oxygen
model.reactions.get_by_id("R009ex").lower_bound = 0 #ethanol
model.reactions.get_by_id("R010ex").lower_bound = 0 #acetate
model.reactions.get_by_id("R011ex").lower_bound = 0 #glucose
model.reactions.get_by_id("R012ex").lower_bound = 0 #urate
model.reactions.get_by_id("R001ex").upper_bound = M #water
model.reactions.get_by_id("R002ex").upper_bound = 0 #phosphate
model.reactions.get_by_id("R003ex").upper_bound = 0 #sucrose
model.reactions.get_by_id("R004ex").upper_bound = 0 #ammonia
model.reactions.get_by_id("R005ex").upper_bound = 0 #sulfate
model.reactions.get_by_id("R006ex").upper_bound = M #protons
model.reactions.get_by_id("R007ex").upper_bound = M #carbon dioxide
model.reactions.get_by_id("R008ex").upper_bound = 0 #oxygen
model.reactions.get_by_id("R009ex").upper_bound = M #ethanol
model.reactions.get_by_id("R010ex").upper_bound = 0 #acetate
model.reactions.get_by_id("R011ex").upper_bound = 0 #glucose
model.reactions.get_by_id("R012ex").upper_bound = M #urate
model.repair()
#solve FBA
solution = model.optimize()
#need to write the shadow prices
output.write(str(trial)+"\t")
output.write(str("SCM\t"))
output.write("{:e}".format(solution.objective_value)+"\t")
output.write("{:e}".format(solution.shadow_prices.X00001__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C04033__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00779__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01173__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01624__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00083__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C17937DHN__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05578__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05579__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01693__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05604__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00355__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00822__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00082__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C17937Eu__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00544__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.X00002__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01179__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C17937Pyo__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00353__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C03427__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05421__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05414__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05430__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05431__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05432__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05435__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C15867__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C08613__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C02094__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C19892__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C08607__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00097__c)+"\t")
output.write("1\n")
trial=trial+1
print("Trial "+str(trial)+" running...\n")
########################################## TRIAL 3 ##########################################
# Carbon-limited sucrose as carbon source, LB(R003ex) = -1 #
#############################################################################################
#set the bounds for exchange reactions
#note that ".lowerbound" does not appear to work, only ".lower_bound"
#note that ".upperbound" does not appear to work, only ".upper_bound"
model.reactions.get_by_id("R001ex").lower_bound = -M #water
model.reactions.get_by_id("R002ex").lower_bound = -M #phosphate
model.reactions.get_by_id("R003ex").lower_bound = -1 #sucrose
model.reactions.get_by_id("R004ex").lower_bound = -M #ammonia
model.reactions.get_by_id("R005ex").lower_bound = -M #sulfate
model.reactions.get_by_id("R006ex").lower_bound = -M #protons
model.reactions.get_by_id("R007ex").lower_bound = 0 #carbon dioxide
model.reactions.get_by_id("R008ex").lower_bound = -M #oxygen
model.reactions.get_by_id("R009ex").lower_bound = 0 #ethanol
model.reactions.get_by_id("R010ex").lower_bound = 0 #acetate
model.reactions.get_by_id("R011ex").lower_bound = 0 #glucose
model.reactions.get_by_id("R012ex").lower_bound = 0 #urate
model.reactions.get_by_id("R001ex").upper_bound = M #water
model.reactions.get_by_id("R002ex").upper_bound = 0 #phosphate
model.reactions.get_by_id("R003ex").upper_bound = 0 #sucrose
model.reactions.get_by_id("R004ex").upper_bound = 0 #ammonia
model.reactions.get_by_id("R005ex").upper_bound = 0 #sulfate
model.reactions.get_by_id("R006ex").upper_bound = M #protons
model.reactions.get_by_id("R007ex").upper_bound = M #carbon dioxide
model.reactions.get_by_id("R008ex").upper_bound = 0 #oxygen
model.reactions.get_by_id("R009ex").upper_bound = M #ethanol
model.reactions.get_by_id("R010ex").upper_bound = 0 #acetate
model.reactions.get_by_id("R011ex").upper_bound = 0 #glucose
model.reactions.get_by_id("R012ex").upper_bound = M #urate
model.repair()
#solve FBA
solution = model.optimize()
#need to write the shadow prices
output.write(str(trial)+"\t")
output.write(str("SCH\t"))
output.write("{:e}".format(solution.objective_value)+"\t")
output.write("{:e}".format(solution.shadow_prices.X00001__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C04033__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00779__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01173__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01624__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00083__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C17937DHN__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05578__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05579__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01693__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05604__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00355__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00822__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00082__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C17937Eu__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00544__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.X00002__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01179__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C17937Pyo__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00353__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C03427__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05421__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05414__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05430__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05431__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05432__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05435__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C15867__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C08613__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C02094__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C19892__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C08607__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00097__c)+"\t")
output.write("1\n")
trial=trial+1
print("Trial "+str(trial)+" running...\n")
########################################## TRIAL 4 ##########################################
# Carbon-limited ethanol as carbon source, LB(R009ex) = -1.5 #
#############################################################################################
#set the bounds for exchange reactions
#note that ".lowerbound" does not appear to work, only ".lower_bound"
#note that ".upperbound" does not appear to work, only ".upper_bound"
model.reactions.get_by_id("R001ex").lower_bound = -M #water
model.reactions.get_by_id("R002ex").lower_bound = -M #phosphate
model.reactions.get_by_id("R003ex").lower_bound = 0 #sucrose
model.reactions.get_by_id("R004ex").lower_bound = -M #ammonia
model.reactions.get_by_id("R005ex").lower_bound = -M #sulfate
model.reactions.get_by_id("R006ex").lower_bound = -M #protons
model.reactions.get_by_id("R007ex").lower_bound = 0 #carbon dioxide
model.reactions.get_by_id("R008ex").lower_bound = -M #oxygen
model.reactions.get_by_id("R009ex").lower_bound = -1.5 #ethanol
model.reactions.get_by_id("R010ex").lower_bound = 0 #acetate
model.reactions.get_by_id("R011ex").lower_bound = 0 #glucose
model.reactions.get_by_id("R012ex").lower_bound = 0 #urate
model.reactions.get_by_id("R001ex").upper_bound = M #water
model.reactions.get_by_id("R002ex").upper_bound = 0 #phosphate
model.reactions.get_by_id("R003ex").upper_bound = 0 #sucrose
model.reactions.get_by_id("R004ex").upper_bound = 0 #ammonia
model.reactions.get_by_id("R005ex").upper_bound = 0 #sulfate
model.reactions.get_by_id("R006ex").upper_bound = M #protons
model.reactions.get_by_id("R007ex").upper_bound = M #carbon dioxide
model.reactions.get_by_id("R008ex").upper_bound = 0 #oxygen
model.reactions.get_by_id("R009ex").upper_bound = M #ethanol
model.reactions.get_by_id("R010ex").upper_bound = 0 #acetate
model.reactions.get_by_id("R011ex").upper_bound = 0 #glucose
model.reactions.get_by_id("R012ex").upper_bound = M #urate
model.repair()
#solve FBA
solution = model.optimize()
#need to write the shadow prices
output.write(str(trial)+"\t")
output.write(str("ECL\t"))
output.write("{:e}".format(solution.objective_value)+"\t")
output.write("{:e}".format(solution.shadow_prices.X00001__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C04033__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00779__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01173__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01624__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00083__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C17937DHN__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05578__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05579__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01693__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05604__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00355__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00822__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00082__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C17937Eu__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00544__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.X00002__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01179__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C17937Pyo__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00353__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C03427__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05421__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05414__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05430__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05431__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05432__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05435__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C15867__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C08613__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C02094__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C19892__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C08607__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00097__c)+"\t")
output.write("1\n")
trial=trial+1
print("Trial "+str(trial)+" running...\n")
########################################## TRIAL 5 ##########################################
# Carbon-limited ethanol as carbon source, LB(R009ex) = -3 #
#############################################################################################
#set the bounds for exchange reactions
#note that ".lowerbound" does not appear to work, only ".lower_bound"
#note that ".upperbound" does not appear to work, only ".upper_bound"
model.reactions.get_by_id("R001ex").lower_bound = -M #water
model.reactions.get_by_id("R002ex").lower_bound = -M #phosphate
model.reactions.get_by_id("R003ex").lower_bound = 0 #sucrose
model.reactions.get_by_id("R004ex").lower_bound = -M #ammonia
model.reactions.get_by_id("R005ex").lower_bound = -M #sulfate
model.reactions.get_by_id("R006ex").lower_bound = -M #protons
model.reactions.get_by_id("R007ex").lower_bound = 0 #carbon dioxide
model.reactions.get_by_id("R008ex").lower_bound = -M #oxygen
model.reactions.get_by_id("R009ex").lower_bound = -3 #ethanol
model.reactions.get_by_id("R010ex").lower_bound = 0 #acetate
model.reactions.get_by_id("R011ex").lower_bound = 0 #glucose
model.reactions.get_by_id("R012ex").lower_bound = 0 #urate
model.reactions.get_by_id("R001ex").upper_bound = M #water
model.reactions.get_by_id("R002ex").upper_bound = 0 #phosphate
model.reactions.get_by_id("R003ex").upper_bound = 0 #sucrose
model.reactions.get_by_id("R004ex").upper_bound = 0 #ammonia
model.reactions.get_by_id("R005ex").upper_bound = 0 #sulfate
model.reactions.get_by_id("R006ex").upper_bound = M #protons
model.reactions.get_by_id("R007ex").upper_bound = M #carbon dioxide
model.reactions.get_by_id("R008ex").upper_bound = 0 #oxygen
model.reactions.get_by_id("R009ex").upper_bound = M #ethanol
model.reactions.get_by_id("R010ex").upper_bound = 0 #acetate
model.reactions.get_by_id("R011ex").upper_bound = 0 #glucose
model.reactions.get_by_id("R012ex").upper_bound = M #urate
model.repair()
#solve FBA
solution = model.optimize()
#need to write the shadow prices
output.write(str(trial)+"\t")
output.write(str("ECM\t"))
output.write("{:e}".format(solution.objective_value)+"\t")
output.write("{:e}".format(solution.shadow_prices.X00001__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C04033__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00779__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01173__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01624__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00083__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C17937DHN__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05578__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05579__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01693__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05604__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00355__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00822__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00082__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C17937Eu__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00544__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.X00002__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01179__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C17937Pyo__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00353__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C03427__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05421__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05414__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05430__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05431__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05432__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05435__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C15867__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C08613__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C02094__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C19892__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C08607__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00097__c)+"\t")
output.write("1\n")
trial=trial+1
print("Trial "+str(trial)+" running...\n")
########################################## TRIAL 6 ##########################################
# Carbon-limited ethanol as carbon source, LB(R009ex) = -6 #
#############################################################################################
#set the bounds for exchange reactions
#note that ".lowerbound" does not appear to work, only ".lower_bound"
#note that ".upperbound" does not appear to work, only ".upper_bound"
model.reactions.get_by_id("R001ex").lower_bound = -M #water
model.reactions.get_by_id("R002ex").lower_bound = -M #phosphate
model.reactions.get_by_id("R003ex").lower_bound = 0 #sucrose
model.reactions.get_by_id("R004ex").lower_bound = -M #ammonia
model.reactions.get_by_id("R005ex").lower_bound = -M #sulfate
model.reactions.get_by_id("R006ex").lower_bound = -M #protons
model.reactions.get_by_id("R007ex").lower_bound = 0 #carbon dioxide
model.reactions.get_by_id("R008ex").lower_bound = -M #oxygen
model.reactions.get_by_id("R009ex").lower_bound = -6 #ethanol
model.reactions.get_by_id("R010ex").lower_bound = 0 #acetate
model.reactions.get_by_id("R011ex").lower_bound = 0 #glucose
model.reactions.get_by_id("R012ex").lower_bound = 0 #urate
model.reactions.get_by_id("R001ex").upper_bound = M #water
model.reactions.get_by_id("R002ex").upper_bound = 0 #phosphate
model.reactions.get_by_id("R003ex").upper_bound = 0 #sucrose
model.reactions.get_by_id("R004ex").upper_bound = 0 #ammonia
model.reactions.get_by_id("R005ex").upper_bound = 0 #sulfate
model.reactions.get_by_id("R006ex").upper_bound = M #protons
model.reactions.get_by_id("R007ex").upper_bound = M #carbon dioxide
model.reactions.get_by_id("R008ex").upper_bound = 0 #oxygen
model.reactions.get_by_id("R009ex").upper_bound = M #ethanol
model.reactions.get_by_id("R010ex").upper_bound = 0 #acetate
model.reactions.get_by_id("R011ex").upper_bound = 0 #glucose
model.reactions.get_by_id("R012ex").upper_bound = M #urate
model.repair()
#solve FBA
solution = model.optimize()
#need to write the shadow prices
output.write(str(trial)+"\t")
output.write(str("ECH\t"))
output.write("{:e}".format(solution.objective_value)+"\t")
output.write("{:e}".format(solution.shadow_prices.X00001__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C04033__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00779__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01173__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01624__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00083__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C17937DHN__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05578__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05579__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01693__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05604__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00355__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00822__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00082__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C17937Eu__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00544__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.X00002__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01179__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C17937Pyo__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00353__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C03427__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05421__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05414__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05430__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05431__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05432__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05435__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C15867__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C08613__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C02094__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C19892__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C08607__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00097__c)+"\t")
output.write("1\n")
trial=trial+1
print("Trial "+str(trial)+" running...\n")
########################################## TRIAL 7 ##########################################
# Carbon-limited acetate as carbon source, LB(R010ex) = -1.5 #
#############################################################################################
#set the bounds for exchange reactions
#note that ".lowerbound" does not appear to work, only ".lower_bound"
#note that ".upperbound" does not appear to work, only ".upper_bound"
model.reactions.get_by_id("R001ex").lower_bound = -M #water
model.reactions.get_by_id("R002ex").lower_bound = -M #phosphate
model.reactions.get_by_id("R003ex").lower_bound = 0 #sucrose
model.reactions.get_by_id("R004ex").lower_bound = -M #ammonia
model.reactions.get_by_id("R005ex").lower_bound = -M #sulfate
model.reactions.get_by_id("R006ex").lower_bound = -M #protons
model.reactions.get_by_id("R007ex").lower_bound = 0 #carbon dioxide
model.reactions.get_by_id("R008ex").lower_bound = -M #oxygen
model.reactions.get_by_id("R009ex").lower_bound = 0 #ethanol
model.reactions.get_by_id("R010ex").lower_bound = -1.5 #acetate
model.reactions.get_by_id("R011ex").lower_bound = 0 #glucose
model.reactions.get_by_id("R012ex").lower_bound = 0 #urate
model.reactions.get_by_id("R001ex").upper_bound = M #water
model.reactions.get_by_id("R002ex").upper_bound = 0 #phosphate
model.reactions.get_by_id("R003ex").upper_bound = 0 #sucrose
model.reactions.get_by_id("R004ex").upper_bound = 0 #ammonia
model.reactions.get_by_id("R005ex").upper_bound = 0 #sulfate
model.reactions.get_by_id("R006ex").upper_bound = M #protons
model.reactions.get_by_id("R007ex").upper_bound = M #carbon dioxide
model.reactions.get_by_id("R008ex").upper_bound = 0 #oxygen
model.reactions.get_by_id("R009ex").upper_bound = M #ethanol
model.reactions.get_by_id("R010ex").upper_bound = 0 #acetate
model.reactions.get_by_id("R011ex").upper_bound = 0 #glucose
model.reactions.get_by_id("R012ex").upper_bound = M #urate
model.repair()
#solve FBA
solution = model.optimize()
#need to write the shadow prices
output.write(str(trial)+"\t")
output.write(str("ACL\t"))
output.write("{:e}".format(solution.objective_value)+"\t")
output.write("{:e}".format(solution.shadow_prices.X00001__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C04033__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00779__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01173__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01624__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00083__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C17937DHN__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05578__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05579__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01693__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05604__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00355__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00822__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00082__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C17937Eu__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00544__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.X00002__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01179__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C17937Pyo__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00353__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C03427__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05421__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05414__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05430__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05431__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05432__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05435__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C15867__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C08613__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C02094__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C19892__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C08607__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00097__c)+"\t")
output.write("1\n")
trial=trial+1
print("Trial "+str(trial)+" running...\n")
########################################## TRIAL 8 ##########################################
# Carbon-limited acetate as carbon source, LB(R010ex) = -3 #
#############################################################################################
#set the bounds for exchange reactions
#note that ".lowerbound" does not appear to work, only ".lower_bound"
#note that ".upperbound" does not appear to work, only ".upper_bound"
model.reactions.get_by_id("R001ex").lower_bound = -M #water
model.reactions.get_by_id("R002ex").lower_bound = -M #phosphate
model.reactions.get_by_id("R003ex").lower_bound = 0 #sucrose
model.reactions.get_by_id("R004ex").lower_bound = -M #ammonia
model.reactions.get_by_id("R005ex").lower_bound = -M #sulfate
model.reactions.get_by_id("R006ex").lower_bound = -M #protons
model.reactions.get_by_id("R007ex").lower_bound = 0 #carbon dioxide
model.reactions.get_by_id("R008ex").lower_bound = -M #oxygen
model.reactions.get_by_id("R009ex").lower_bound = 0 #ethanol
model.reactions.get_by_id("R010ex").lower_bound = -3 #acetate
model.reactions.get_by_id("R011ex").lower_bound = 0 #glucose
model.reactions.get_by_id("R012ex").lower_bound = 0 #urate
model.reactions.get_by_id("R001ex").upper_bound = M #water
model.reactions.get_by_id("R002ex").upper_bound = 0 #phosphate
model.reactions.get_by_id("R003ex").upper_bound = 0 #sucrose
model.reactions.get_by_id("R004ex").upper_bound = 0 #ammonia
model.reactions.get_by_id("R005ex").upper_bound = 0 #sulfate
model.reactions.get_by_id("R006ex").upper_bound = M #protons
model.reactions.get_by_id("R007ex").upper_bound = M #carbon dioxide
model.reactions.get_by_id("R008ex").upper_bound = 0 #oxygen
model.reactions.get_by_id("R009ex").upper_bound = M #ethanol
model.reactions.get_by_id("R010ex").upper_bound = 0 #acetate
model.reactions.get_by_id("R011ex").upper_bound = 0 #glucose
model.reactions.get_by_id("R012ex").upper_bound = M #urate
model.repair()
#solve FBA
solution = model.optimize()
#need to write the shadow prices
output.write(str(trial)+"\t")
output.write(str("ACM\t"))
output.write("{:e}".format(solution.objective_value)+"\t")
output.write("{:e}".format(solution.shadow_prices.X00001__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C04033__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00779__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01173__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01624__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00083__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C17937DHN__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05578__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05579__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01693__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05604__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00355__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00822__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00082__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C17937Eu__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00544__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.X00002__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01179__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C17937Pyo__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00353__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C03427__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05421__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05414__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05430__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05431__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05432__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05435__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C15867__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C08613__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C02094__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C19892__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C08607__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00097__c)+"\t")
output.write("1\n")
trial=trial+1
print("Trial "+str(trial)+" running...\n")
########################################## TRIAL 9 ##########################################
# Carbon-limited acetate as carbon source, LB(R010ex) = -6 #
#############################################################################################
#set the bounds for exchange reactions
#note that ".lowerbound" does not appear to work, only ".lower_bound"
#note that ".upperbound" does not appear to work, only ".upper_bound"
model.reactions.get_by_id("R001ex").lower_bound = -M #water
model.reactions.get_by_id("R002ex").lower_bound = -M #phosphate
model.reactions.get_by_id("R003ex").lower_bound = 0 #sucrose
model.reactions.get_by_id("R004ex").lower_bound = -M #ammonia
model.reactions.get_by_id("R005ex").lower_bound = -M #sulfate
model.reactions.get_by_id("R006ex").lower_bound = -M #protons
model.reactions.get_by_id("R007ex").lower_bound = 0 #carbon dioxide
model.reactions.get_by_id("R008ex").lower_bound = -M #oxygen
model.reactions.get_by_id("R009ex").lower_bound = 0 #ethanol
model.reactions.get_by_id("R010ex").lower_bound = -6 #acetate
model.reactions.get_by_id("R011ex").lower_bound = 0 #glucose
model.reactions.get_by_id("R012ex").lower_bound = 0 #urate
model.reactions.get_by_id("R001ex").upper_bound = M #water
model.reactions.get_by_id("R002ex").upper_bound = 0 #phosphate
model.reactions.get_by_id("R003ex").upper_bound = 0 #sucrose
model.reactions.get_by_id("R004ex").upper_bound = 0 #ammonia
model.reactions.get_by_id("R005ex").upper_bound = 0 #sulfate
model.reactions.get_by_id("R006ex").upper_bound = M #protons
model.reactions.get_by_id("R007ex").upper_bound = M #carbon dioxide
model.reactions.get_by_id("R008ex").upper_bound = 0 #oxygen
model.reactions.get_by_id("R009ex").upper_bound = M #ethanol
model.reactions.get_by_id("R010ex").upper_bound = 0 #acetate
model.reactions.get_by_id("R011ex").upper_bound = 0 #glucose
model.reactions.get_by_id("R012ex").upper_bound = M #urate
model.repair()
#solve FBA
solution = model.optimize()
#need to write the shadow prices
output.write(str(trial)+"\t")
output.write(str("ACH\t"))
output.write("{:e}".format(solution.objective_value)+"\t")
output.write("{:e}".format(solution.shadow_prices.X00001__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C04033__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00779__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01173__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01624__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00083__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C17937DHN__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05578__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05579__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01693__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05604__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00355__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00822__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00082__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C17937Eu__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00544__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.X00002__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01179__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C17937Pyo__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00353__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C03427__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05421__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05414__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05430__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05431__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05432__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05435__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C15867__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C08613__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C02094__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C19892__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C08607__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00097__c)+"\t")
output.write("1\n")
trial=trial+1
print("Trial "+str(trial)+" running...\n")
########################################## TRIAL 10 #########################################
# Carbon-limited glucose as carbon source, LB(R011ex) = -0.5 #
#############################################################################################
#set the bounds for exchange reactions
#note that ".lowerbound" does not appear to work, only ".lower_bound"
#note that ".upperbound" does not appear to work, only ".upper_bound"
model.reactions.get_by_id("R001ex").lower_bound = -M #water
model.reactions.get_by_id("R002ex").lower_bound = -M #phosphate
model.reactions.get_by_id("R003ex").lower_bound = 0 #sucrose
model.reactions.get_by_id("R004ex").lower_bound = -M #ammonia
model.reactions.get_by_id("R005ex").lower_bound = -M #sulfate
model.reactions.get_by_id("R006ex").lower_bound = -M #protons
model.reactions.get_by_id("R007ex").lower_bound = 0 #carbon dioxide
model.reactions.get_by_id("R008ex").lower_bound = -M #oxygen
model.reactions.get_by_id("R009ex").lower_bound = 0 #ethanol
model.reactions.get_by_id("R010ex").lower_bound = 0 #acetate
model.reactions.get_by_id("R011ex").lower_bound = -0.5 #glucose
model.reactions.get_by_id("R012ex").lower_bound = 0 #urate
model.reactions.get_by_id("R001ex").upper_bound = M #water
model.reactions.get_by_id("R002ex").upper_bound = 0 #phosphate
model.reactions.get_by_id("R003ex").upper_bound = 0 #sucrose
model.reactions.get_by_id("R004ex").upper_bound = 0 #ammonia
model.reactions.get_by_id("R005ex").upper_bound = 0 #sulfate
model.reactions.get_by_id("R006ex").upper_bound = M #protons
model.reactions.get_by_id("R007ex").upper_bound = M #carbon dioxide
model.reactions.get_by_id("R008ex").upper_bound = 0 #oxygen
model.reactions.get_by_id("R009ex").upper_bound = M #ethanol
model.reactions.get_by_id("R010ex").upper_bound = 0 #acetate
model.reactions.get_by_id("R011ex").upper_bound = 0 #glucose
model.reactions.get_by_id("R012ex").upper_bound = M #urate
model.repair()
#solve FBA
solution = model.optimize()
#need to write the shadow prices
output.write(str(trial)+"\t")
output.write(str("GCL\t"))
output.write("{:e}".format(solution.objective_value)+"\t")
output.write("{:e}".format(solution.shadow_prices.X00001__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C04033__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00779__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01173__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01624__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00083__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C17937DHN__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05578__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05579__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01693__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05604__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00355__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00822__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00082__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C17937Eu__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00544__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.X00002__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01179__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C17937Pyo__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00353__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C03427__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05421__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05414__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05430__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05431__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05432__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05435__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C15867__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C08613__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C02094__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C19892__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C08607__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00097__c)+"\t")
output.write("1\n")
trial=trial+1
print("Trial "+str(trial)+" running...\n")
########################################## TRIAL 11 #########################################
# Carbon-limited glucose as carbon source, LB(R011ex) = -1 #
#############################################################################################
#set the bounds for exchange reactions
#note that ".lowerbound" does not appear to work, only ".lower_bound"
#note that ".upperbound" does not appear to work, only ".upper_bound"
model.reactions.get_by_id("R001ex").lower_bound = -M #water
model.reactions.get_by_id("R002ex").lower_bound = -M #phosphate
model.reactions.get_by_id("R003ex").lower_bound = 0 #sucrose
model.reactions.get_by_id("R004ex").lower_bound = -M #ammonia
model.reactions.get_by_id("R005ex").lower_bound = -M #sulfate
model.reactions.get_by_id("R006ex").lower_bound = -M #protons
model.reactions.get_by_id("R007ex").lower_bound = 0 #carbon dioxide
model.reactions.get_by_id("R008ex").lower_bound = -M #oxygen
model.reactions.get_by_id("R009ex").lower_bound = 0 #ethanol
model.reactions.get_by_id("R010ex").lower_bound = 0 #acetate
model.reactions.get_by_id("R011ex").lower_bound = -1 #glucose
model.reactions.get_by_id("R012ex").lower_bound = 0 #urate
model.reactions.get_by_id("R001ex").upper_bound = M #water
model.reactions.get_by_id("R002ex").upper_bound = 0 #phosphate
model.reactions.get_by_id("R003ex").upper_bound = 0 #sucrose
model.reactions.get_by_id("R004ex").upper_bound = 0 #ammonia
model.reactions.get_by_id("R005ex").upper_bound = 0 #sulfate
model.reactions.get_by_id("R006ex").upper_bound = M #protons
model.reactions.get_by_id("R007ex").upper_bound = M #carbon dioxide
model.reactions.get_by_id("R008ex").upper_bound = 0 #oxygen
model.reactions.get_by_id("R009ex").upper_bound = M #ethanol
model.reactions.get_by_id("R010ex").upper_bound = 0 #acetate
model.reactions.get_by_id("R011ex").upper_bound = 0 #glucose
model.reactions.get_by_id("R012ex").upper_bound = M #urate
model.repair()
#solve FBA
solution = model.optimize()
#need to write the shadow prices
output.write(str(trial)+"\t")
output.write(str("GCM\t"))
output.write("{:e}".format(solution.objective_value)+"\t")
output.write("{:e}".format(solution.shadow_prices.X00001__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C04033__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00779__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01173__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01624__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00083__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C17937DHN__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05578__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05579__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01693__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05604__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00355__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00822__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00082__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C17937Eu__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00544__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.X00002__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01179__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C17937Pyo__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00353__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C03427__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05421__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05414__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05430__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05431__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05432__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05435__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C15867__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C08613__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C02094__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C19892__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C08607__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00097__c)+"\t")
output.write("1\n")
trial=trial+1
print("Trial "+str(trial)+" running...\n")
########################################## TRIAL 12 #########################################
# Carbon-limited glucose as carbon source, LB(R011ex) = -2 #
#############################################################################################
#set the bounds for exchange reactions
#note that ".lowerbound" does not appear to work, only ".lower_bound"
#note that ".upperbound" does not appear to work, only ".upper_bound"
model.reactions.get_by_id("R001ex").lower_bound = -M #water
model.reactions.get_by_id("R002ex").lower_bound = -M #phosphate
model.reactions.get_by_id("R003ex").lower_bound = 0 #sucrose
model.reactions.get_by_id("R004ex").lower_bound = -M #ammonia
model.reactions.get_by_id("R005ex").lower_bound = -M #sulfate
model.reactions.get_by_id("R006ex").lower_bound = -M #protons
model.reactions.get_by_id("R007ex").lower_bound = 0 #carbon dioxide
model.reactions.get_by_id("R008ex").lower_bound = -M #oxygen
model.reactions.get_by_id("R009ex").lower_bound = 0 #ethanol
model.reactions.get_by_id("R010ex").lower_bound = 0 #acetate
model.reactions.get_by_id("R011ex").lower_bound = -2 #glucose
model.reactions.get_by_id("R012ex").lower_bound = 0 #urate
model.reactions.get_by_id("R001ex").upper_bound = M #water
model.reactions.get_by_id("R002ex").upper_bound = 0 #phosphate
model.reactions.get_by_id("R003ex").upper_bound = 0 #sucrose
model.reactions.get_by_id("R004ex").upper_bound = 0 #ammonia
model.reactions.get_by_id("R005ex").upper_bound = 0 #sulfate
model.reactions.get_by_id("R006ex").upper_bound = M #protons
model.reactions.get_by_id("R007ex").upper_bound = M #carbon dioxide
model.reactions.get_by_id("R008ex").upper_bound = 0 #oxygen
model.reactions.get_by_id("R009ex").upper_bound = M #ethanol
model.reactions.get_by_id("R010ex").upper_bound = 0 #acetate
model.reactions.get_by_id("R011ex").upper_bound = 0 #glucose
model.reactions.get_by_id("R012ex").upper_bound = M #urate
model.repair()
#solve FBA
solution = model.optimize()
#need to write the shadow prices
output.write(str(trial)+"\t")
output.write(str("GCH\t"))
output.write("{:e}".format(solution.objective_value)+"\t")
output.write("{:e}".format(solution.shadow_prices.X00001__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C04033__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00779__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01173__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01624__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00083__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C17937DHN__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05578__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05579__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01693__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05604__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00355__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00822__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00082__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C17937Eu__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00544__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.X00002__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C01179__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C17937Pyo__e)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00353__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C03427__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05421__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05414__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05430__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05431__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05432__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C05435__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C15867__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C08613__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C02094__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C19892__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C08607__c)+"\t")
output.write("{:e}".format(solution.shadow_prices.C00097__c)+"\t")
output.write("1\n")
trial