inst/clusterProfiler/analyseTSVwithArgs.R

In protViz/prora: ORA, sigORA and GSEA functionalities for proteomic data

# Author W Wolski
# this script analyses all projects in file output_MaxQuant_info_WSpecies.csv

#Rscript analyseTSVwithArgs.R DPAprotein_dist DPA FALSE FALSE  &> log_analyseTSVproteinDPA_dist.log &
#Rscript analyseTSVwithArgs.R DPApeptpide_dist DPA TRUE FALSE  &> log_analyseTSVpeptideDPA_dist.log &
#Rscript analyseTSVwithArgs.R DPAprotein_dist_JK DPA FALSE TRUE  &> log_analyseTSVproteinDPA_dist_JK.log &
#Rscript analyseTSVwithArgs.R DPApeptide_dist_JK DPA TRUE TRUE  &> log_analyseTSVpeptideDPA_dist_JK.log &

#Rscript analyseTSVwithArgs.R HCpeptide_dist hclust_deepsplit TRUE FALSE  &> log_analyseTSVpeptideHCLUST_dist.log &
#Rscript analyseTSVwithArgs.R HCprotein_dist hclust_deepsplit FALSE FALSE  &> log_analyseTSVproteinHCLUST_dist.log &
#Rscript analyseTSVwithArgs.R HCpeptide_dist_JK hclust_deepsplit TRUE TRUE  &> log_analyseTSVpeptideHCLUST_dist_JK.log &
#Rscript analyseTSVwithArgs.R HCprotein_dist_JK hclust_deepsplit FALSE TRUE  &> log_analyseTSVproteinHCLUST_dist_JK.log &


library(tidyverse)
library(readr)

args = commandArgs(trailingOnly = TRUE)

parameters <- list()
if (length(args) == 4) {
  parameters$clustalg <- args[2]
  parameters$outfolder <- args[1]
  parameters$peptide <- as.logical(args[3])
  parameters$JK <- as.logical(args[4])
  print(parameters)
}else{
  parameters$outfolder <- "testing"
  parameters$clustalg <- "hclust_deepsplit"
  parameters$peptide <- TRUE
  parameters$JK <- TRUE
}

tmp <- readr::read_csv("output_MaxQuant_info_WSpecies.csv")
tmp$project_ID <-  gsub("/srv/www/htdocs/(p[0-9]{1,5})/bfabric/.*","\\1",tmp$path_to_zip)

human <- tmp %>% filter(species == "human" & n_inputs >= 8)

if (Sys.info()["sysname"] == "Windows") {
  human$windowpaths <- gsub("/srv/www/htdocs", "y:", human$path_to_zip)
  RscriptExe <- "c:/Program Files/R/R-4.1.1/bin/Rscript.exe"
  stopifnot(file.exists(RscriptExe))
  rscriptlocation <- "runscriptLocal.R"
}else{
  human$windowpaths <- human$path_to_zip
  RscriptExe <- "/usr/bin/Rscript"
  rscriptlocation <- "/scratch/CLUSTERPROFILER/clusterprofileron33/runscriptLocal.R"
}


for (i in seq_len(nrow(human))) {
  print(i)

  path <- human$windowpaths[i]
  workunitid <- human$workunitid[i]
  projectid <- human$project_ID[i]
  message(path, "\nworkunitid : ", workunitid,"\nprojectid : ", projectid)
  if (!file.exists(path)) {
    print(path)
  } else if (TRUE) {
    arguments <- c(rsrcipt = rscriptlocation,
                   path2zip = path,
                   organizm =  "Homo_sapiens",
                   outfolder = parameters$outfolder,
                   clustalg = parameters$clustalg,
                   wunitID = workunitid,
                   projektID = projectid,
                   ispeptide = parameters$peptide,
                   jackknife = parameters$JK)

    dput(arguments, file = "args.R")
    res <- system2(RscriptExe, args = arguments)

    if (res > 0) {
      print("ERROR START running script failed")
      cat(paste("ERROR : ", arguments ,"\n"))
      print("ERROR END")
    }
  }
}

#path <- "y:/p2621/bfabric/Proteomics/MaxQuant/2018/2018-10/2018-10-05/workunit_175797/721705.zip"
#path <- "y:/p2673/bfabric/Proteomics/MaxQuant/2021/2021-01/2021-01-19/workunit_256172/1792120.zip"
#path <-  "y:/p2954/bfabric/Proteomics/MaxQuant/2019/2019-01/2019-01-09/workunit_187912/1068470.zip"
#path <- "y:/p2865/bfabric/Proteomics/MaxQuant/2020/2020-01/2020-01-13/workunit_234979/1462850.zip"


if(FALSE){
  path <- "/srv/www/htdocs/p2702/bfabric/Proteomics/MaxQuant/2019/2019-03/2019-03-14/workunit_194381/1163583.zip"
  #path <- "y:/p2961/bfabric/Proteomics/MaxQuant/2019/2019-06/2019-06-23/workunit_200319/1292787.zip"
  arguments <- c("runscriptLocal.R", path, "human","test" ,"DPA", "194381", "p2702", TRUE, FALSE)

  commandArgs <- function(...){ return(arguments[-1]) }
  commandArgs()
  source("runscriptLocal.R")
}