Skip to content
Snippets Groups Projects
Commit e870f9a7 authored by Sajjad Ghaffarinasabsharabiani's avatar Sajjad Ghaffarinasabsharabiani
Browse files

Delete compGrowth.R

parent 50be0df9
Branches
Tags
No related merge requests found
#!/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)
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment