dlac_v9 debuggig

bash/lsf_bioinfo_utils.sh

@@ -19,6 +19,32 @@ mmFastqc(){
 export -f mmFastqc
 
 
+## count reads in all  fastq and fastq.gz files in the current directory
+mmCountFastGzReads(){
+#    filePattern=$1
+    filePattern=".fastq.gz"
+    for fastqFile in *$filePattern ; do
+        echo processing $fastqFile
+#        echo "countGzipReads $fastqFile | sed -e s/^/${fastqFile%%$filePattern},/g >> readCounts.txt"
+        bsub -J countReads "countGzipReads $fastqFile | sed -e s/^/${fastqFile%%.fastq.gz},/g >> readCounts.txt" | joblist .countreads_jobs
+#        countGzipReads $fastqFile | sed -e s/^/${fastqFile%%.fastq.gz},/g >> readCounts.txt
+    done
+    wait4jobs .countreads_jobs
+
+    ## create a plot
+    echo '
+    devtools::source_url("http://dl.dropbox.com/u/113630701/rlibs/base-commons.R")
+
+    readCounts <- subset(read.csv("readCounts.txt", h=F), select=-2)
+    names(readCounts) <- c("file", "num_reads")
+    gg <- ggplot(readCounts, aes(file, num_reads)) + geom_bar(stat="identity") + ggtitle(paste("read counts in\n", getwd())) + coord_flip() + scale_y_continuous(labels=comma)
+    ggsave("read_counts.png", gg, width=8)
+    ' | R -q --vanilla
+}
+export -f mmCountFastGzReads
+
+
+
 ### Create a cuffdb on a network of lustre file-systen
 MakeCuffdb() {
     if [ $# -ne 2 ]; then echo "Usage: MakeCuffdb <gtffile> <genomebuild>"; return; fi