ExtractProtocol_v2.R
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#!/usr/bin/env Rscript
library("optparse")
library("GEOquery")
source("extraction_functions.R")
#-------------------------------------------------------------------------------
# Objective
# Extract banglines text-content from previous GSEnnn.soft.gz files
#
# Input parameters
# --d download dir with GSE/GSEnnn.soft.gz files
# --i GSE information file (gse, gsm columns)
#
# Parameters examples
# -d ../download/srr_galagan/
# -o ../output/srr_galagan
# -i ../input/normalized_srr-gsm_des_v4.tsv
# -b ../input/listMetaCampo.txt
# -r ../reports/srr_galagan/extract_report.txt
#
# Example
# nohup Rscript ExtractProtocol_v2.R -d ../download/srr_galagan/ -o ../outputs/srr_galagan -i ../input/normalized_srr-gsm_des_v4.tsv -b ../input/listMetaCampo.txt -r ../reports/srr_galagan/extract_report.txt > extract_nohup.out &
#
#######################################################################################
#-----------------------------------------ARGS-----------------------------------------
#######################################################################################
option_list = list(
make_option(c("-d", "--downloadPath"),type="character", default=NULL,
help="download directory", metavar="character"),
make_option(c("-o", "--outputPath"), type="character", default=NULL,
help="directory to output files", metavar="character"),
make_option(c("-i", "--infoFile"), type="character", default=NULL,
help="GSE id information file", metavar="character"),
make_option(c("-b", "--banglines"), type="character", default=NULL,
help="banglines file", metavar="character"),
make_option(c("-r", "--report"), type="character", default=NULL,
help="extraccion report file", metavar="character")
);
opt_parser = OptionParser(option_list=option_list);
opt = parse_args(opt_parser);
if (!length(opt)){
print_help(opt_parser)
stop("At least one argument must be supplied (input file).n", call.=FALSE)
}
#######################################################################################
#-----------------------------------------MAIN-----------------------------------------
#######################################################################################
## Input files and output directories
odir <- opt$outputPath
# Download dir
ddir <- opt$downloadPath
# Baglines list file
bglsfile <- opt$banglines
# GSE information file
infoFile <- opt$infoFile
## Load main variables
# Baglines
bglslist <- readr::read_tsv( bglsfile )
bglsBase <- sapply( bglslist, GetBaseBagline )
# GSE-GSM
gseInfo <- read.table( infoFile,header = T, sep = "\t" )
gseInfo <- gseInfo[complete.cases(gseInfo),]
## Extraction
sink(opt$report, append = FALSE, split = FALSE)
cat("total gse id: ", (length(unique(gseInfo$gse))), "\n")
cat("total gsm id: ", (length(unique(gseInfo$gsm))), "\n")
for (geoid in unique(gseInfo$gse)) {
print(geoid)
## Filter GSMs
subs <- as.vector(gseInfo$gsm[which(geoid == gseInfo$gse)])
report <- tryCatch(
ExtractMetafields( geoid, subs, ddir, odir, bglsBase),
error = function( e ) return( "extraccion failed" ) )
print(report)
}
cat("extracted gsm id: ", length(list.files(opt$outputPath, recursive = TRUE)))