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networkComplexityBigg/qc/compGrowth.R

+#!/usr/bin/Rscript
+library(sybil)
+library(sybilSBML)
+library(sybilSWITCH)
+library(parallel)
+
+eco <- list()
+print(load("~/workspace/models/iAF1260_the-seed-adaption.Rdata"))
+eco$seed <- upgradeModelorg(iAFseed)
+
+load("../models/universalBiGG.ver1.1.Rdata")
+eco$bigg <- changeObjFunc(rmReact(uni1.1, setdiff(react_id(uni1.1), modelReactMap$iAF1260)), modelBiomassMapSelection["iAF1260"])
+
+#load("../modelsCheck/checkedModels.Rdata")
+#eco$biggChecked <- allModels$iAF1260
+
+
+print(load("../sourceData/seed.mobd.media.Rdata"))
+print(load("../sourceData/balazs.media.Rdata"))
+
+
+print(load("../sourceData/seed.mobd.media.Rdata"))
+print(load("../sourceData/balazs.media.Rdata"))
+media <- list()
+media$seed <- c(seed.mobd.media, balazs.media)
+media$bigg <- get(load("../convertMedia/mediaBiGG.Rdata"))
+
+stopifnot(setequal(names(media$seed), names(media$bigg)))
+mediaNames <- names(media$seed)
+media <- lapply(media, function(x) x[mediaNames])
+
+namespace <- c(bigg="bigg", seed="seed")#, biggChecked="bigg")
+mnames <- names(eco)
+names(mnames) <- names(eco)
+
+
+
+#mediaArm <- function(id="", medium){
+#	m <- eco[[id]]
+#	me <- media[[namespace[id]]]
+#	
+#	ex <- findExchReact(m)
+#	lowbnd(m)[react_pos(ex)] <- -10
+#	exMap <- gsub("\\[.+$", "", met_id(ex))
+#	
+#	
+#	sp <- suggestedArmSolverSettings()
+#	sp$CPX_PARAM_EPINT <- 1e-9
+#	sp$CPX_PARAM_EPRHS <- 1e-9
+#	
+#	ar <- setdiff(react_pos(ex), react_pos(ex)[exMap %in% me[[medium]]])
+#	
+#	arm <- optimizeProb(m, 
+#		additionalReact=ar,
+#		biomassThreshold=0.1,
+#		algorithm="arm",
+#		solverParm=sp)
+#	
+#	fluxes <- getArmReactionFluxes(m, arm)[react_pos(ex)]
+#	names(fluxes) <- met_id(ex)
+#	browser()
+#	fluxes[fluxes < -1e-9]
+#}
+
+#add <- mediaArm("bigg", "C_cpd00751")
+
+
+
+df <- as.data.frame(lapply(mnames, function(e){
+	m <- eco[[e]]
+	
+	ex <- findExchReact(m)
+	
+	react <- list(react_pos(ex))
+	mid <- namespace[e]
+	r <- rep(list(react_pos(ex)), length(media[[mid]]))
+	
+	exMap <- gsub("\\[.+$", "", met_id(ex))
+	lb <- lapply(media[[mid]], function(x){
+		v <- rep(0, length(exMap))
+		v[exMap %in% x] <- -10
+		print(x[!x %in% exMap])
+		v
+	})
+	
+	ub <- rep(list(uppbnd(m)[react_pos(ex)]), length(media[[mid]]))
+	opt <- optimizer(m, react=r, lb=lb, ub=ub, verboseMode=1)
+	obj <- opt$obj
+	obj[checkSolStat(opt$stat)] <- 0
+	return(round(obj, digits=6))
+}))
+
+rownames(df) <- mediaNames
+
+growth <- cbind(name=rownames(df), as.data.frame(df > 1e-6))
+
+
+dfg1 <- data.frame(expand.grid(seed=c(T, F), bigg=c(T, F)))
+dfg1$sums <- apply(dfg1, 1, function(x) sum(growth[,"seed"] == x[1] & growth[,"bigg"] == x[2] ))
+print(dfg1)
+
+stopifnot(sum(dfg1[2:3, 3])==0)
+
+#dfg1 <- data.frame(expand.grid(seed=c(T, F), bigg=c(T, F)))
+#dfg1$sums <- apply(dfg1, 1, function(x) sum(growth[,"seed"] == x[1] & growth[,"biggChecked"] == x[2] ))
+#print(dfg1)
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