Delete compGrowth.R

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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