rm(list = ls())
library(dplyr)
library(ccube)
library(doParallel)
library(ggplot2)
library(tidyr)
library(gridExtra)
options(stringsAsFactors = F)
registerDoParallel(cores=3)
set.seed(1234)
numOfClusterPool = 1:7
numOfRepeat = 1
icgc <- "~/debug_pcawg_samples_sv/svclone_paper_20181127/"
dataFolders <- dir(icgc, full.names = T)
sampleNames <- dir(icgc)
bugSamples <- c()
bugdataFolders <- c()
for (ii in seq_along(sampleNames)) {
sampleName <- sampleNames[ii]
dataFolder <- dataFolders[ii]
if (! "ccube_out/ccube_sv_results.RData" %in% dir(dataFolder, recursive = T) ) {
bugSamples <- c(bugSamples, sampleName)
bugdataFolders <- c(bugdataFolders, dataFolder)
}
}
allDebugFolder <- "~/debug_pcawg_samples_sv/debuged_samples_all_full_run_low_iter_10_test"
if (! dir.exists(allDebugFolder) ) {
dir.create(allDebugFolder)
}
singleEventSamples <- c()
problemSamples <- c()
inputProblemSamples <- c()
for (ii in seq_along(sampleNames)) {
cat(ii, "\n")
sampleName <- sampleNames[ii]
dataFolder <- dataFolders[ii]
resultsFolder <- paste0(allDebugFolder,"/", sampleName)
if (! dir.exists(resultsFolder) ) {
dir.create(resultsFolder)
}
inputFn <- paste0(dataFolder, "/", sampleName, "_ccube_sv_input.txt")
mydata <- try( read.delim(inputFn), T)
if ( is.data.frame(mydata) ) {
if (nrow(mydata) == 1) {
singleEventSamples <- c(singleEventSamples, sampleName)
cat("single event", file = paste0(resultsFolder, "/single_event_sample") )
}
ccubeRes <- try(
RunCcubePipeline(ssm = mydata, modelSV = T,
numOfClusterPool = numOfClusterPool,
numOfRepeat = numOfRepeat, multiCore =T,
runAnalysis = T, runQC = T, maxiter = 10),
T
)
if (is.list (ccubeRes) ) {
fn = paste0(resultsFolder, "/ccube_sv_results.RDdata")
save(ccubeRes, file = fn)
if (nrow(mydata) > 1) {
fn = paste0(resultsFolder, "/ccube_sv_results.pdf")
MakeCcubeStdPlot_sv(res = ccubeRes$res, ssm = ccubeRes$ssm, printPlot = T, fn = fn)
}
} else {
cat(ccubeRes, file = paste0(resultsFolder, "/bug_info_ccube.txt"))
if (nrow(mydata) > 1) {
problemSamples <- c(problemSamples, sampleName)
cat("problematic sample", file = paste0(resultsFolder, "/problematic_sample") )
}
}
} else {
inputProblemSamples <- c(inputProblemSamples, sampleName)
cat(mydata, file = paste0(resultsFolder, "/bug_info_mydata.txt"))
}
}
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