# HG changeset patch # User stef # Date 1403084702 14400 # Node ID 647143d0c884e540eeef6f1b590272a40d22de4f # Parent 4c4e4d88779c854646596a277712ecd7b3786fc2 Uploaded diff -r 4c4e4d88779c -r 647143d0c884 QDNAseq.R --- a/QDNAseq.R Wed Jun 18 05:33:04 2014 -0400 +++ b/QDNAseq.R Wed Jun 18 05:45:02 2014 -0400 @@ -116,10 +116,8 @@ sampleCount <- length( regionsList ) sampleNames <- names( regionsList ) - systemUser <- system("whoami",T) bedgraphColumns <- c( 'chr', 'start', 'end', 'segmentval' ) - - cat( MAIN_NAME, " Hello ", systemUser, "!!\n", sep="") + cat( MAIN_NAME, " There are ", sampleCount, " samples found in input list...\n", sep="") for ( sample in sampleNames ){ @@ -179,14 +177,17 @@ DECIMALS <- 3 WEB_LINK <- 'http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html' + + catMsg( "Starting QDNAseq wrapper" ) catMsg( "Loading R libraries" ) suppressWarnings( suppressMessages( library( QDNAseq, quietly = TRUE ) ) ) suppressWarnings( suppressMessages( library( CGHcall, quietly = TRUE ) ) ) +systemUser <- system("whoami",T) qdnaseqVersion <- packageDescription( "QDNAseq" )$Version -qdnaseqDate <- packageDescription( "QDNAseq" )$Date -catMsg( paste("QDNAseq info: version(", qdnaseqVersion, ") and date (", qdnaseqDate, ")", sep="") ) +catMsg( c(" Hello ", systemUser ) ) +catMsg( c("QDNAseq version loaded: ", qdnaseqVersion) ) ## only one param: the tmp config file cmdLineArgs <- commandArgs(TRUE) @@ -350,13 +351,9 @@ plotted_images[[ sample ]][[ 'region_count' ]] <- region_count } - ## add read counts - catMsg( "Used") - catMsg( usedReads ) - + ## add USED read counts plotted_images[[ sample ]][[ 'usedReads' ]] <- usedReads } -#cat( MAIN_NAME, "PLOTTED_IMAGES: ", names(plotted_images), "\n", sep="" ) if ( doCall ){ saveRDS( regions, robjRegionPath )