def main(path2template, resultsPath, runs):
import gzip
tmpLP = metabolism.Metabolism(util.ImportCplex(path2template))
tmpLP.setReactionObjectiveMinimizeRest('R("R_Ec_biomass_iAF1260_core_59p81M")')
include = ('R("Mhb_Transp")',
'R("Mna1b_Transp")',
'R("Mkb_Transp")',
'R("Mca2b_Transp")',
'R("Mcu2b_Transp")',
'R("Mmg2b_Transp")',
'R("Mzn2b_Transp")',
'R("Mmobdb_Transp")',
'R("Mfe2b_Transp")',
'R("Mfe3b_Transp")',
'R("Mcobalt2b_Transp")',
'R("Mmn2b_Transp")',
'R("Mclb_Transp")')
lp = randomMedia.Almaas(copy.copy(tmpLP), alwaysInc=include)
print lp.lp
f = lp.generateFluxdist()
for item in range(runs):
f = lp.generateFluxdist()
stringDump = randomMedia.dict2tsv(lp.currDict) + "\n" + f.tsv()
print stringDump
path = resultsPath + "iAf1260_fluxDist_" + str(item) + ".tsv.gz"
lp.lp.initialize()
gzip.open(path, 'w').write(stringDump)
def main(path2template, resultsPath, runs):
import gzip
tmpLP = metabolism.Metabolism(util.ImportCplex(path2template))
tmpLP.setReactionObjectiveMinimizeRest('R("R_Ec_biomass_iAF1260_core_59p81M")')
lp = copy.copy(tmpLP)
richMed = generateRichMedium(lp.getTransporters())
print richMed
lp.modifyColumnBounds(richMed)
richFluxDist = lp.fba()
stringDump = randomMedia.dict2tsv(richMed) + "\n" + richFluxDist.tsv()
print stringDump
path = resultsPath + "iAf1260_fluxDist_RichMedium.tsv.gz"
gzip.open(path, 'w').write(stringDump)
def main(lp, stub):
include = ('R("Mhb_Transp")',
'R("Mna1b_Transp")',
'R("Mkb_Transp")',
'R("Mca2b_Transp")',
'R("Mcu2b_Transp")',
'R("Mmg2b_Transp")',
'R("Mzn2b_Transp")',
'R("Mmobdb_Transp")',
'R("Mfe2b_Transp")',
'R("Mfe3b_Transp")',
'R("Mcobalt2b_Transp")',
'R("Mmn2b_Transp")',
'R("Mclb_Transp")')
lp = randomMedia.Almaas(lp, alwaysInc=include)
f = lp.generateFluxdist()
stringDump = randomMedia.dict2tsv(lp.currDict) + "\n" + f.active_tsv()
path = "/Users/niko/tmp/" + "iAf1260_fluxDist_" + str(stub) + ".tsv.gz"
gzip.open(path, 'w').write(stringDump)
del(lp)
return stub