diff --git a/networkComplexityBigg/qc/compGrowth.R b/networkComplexityBigg/qc/compGrowth.R deleted file mode 100644 index f50fd4c2d2d6325bf111f5df6931dad81b2f1f00..0000000000000000000000000000000000000000 --- a/networkComplexityBigg/qc/compGrowth.R +++ /dev/null @@ -1,149 +0,0 @@ -#!/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) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -