more flexible bam correlation wrapper

dge_workflow/dge_utils.sh

@@ -185,20 +185,28 @@ export -f dge_tophat_se
 
 dge_bam_correlate(){
 
-if [ $# -ne 1 ]; then
-    echo "Usage: dge_bam_correlate <bam_directory>" >&2 ; return;
+if [ $# -eq 0 ]; then
+    echo "Usage: dge_bam_correlate <bam_directory>" >&2 ;
+    echo "Usage: dge_bam_correlate <bam_files...>" >&2 ;
+    return;
 fi
 
 local bamDir=$1
 
-bamFiles=$(find $bamDir | grep ".bam$" | grep -v "unmapped" | sort)
-bamLabels=$(echo "$bamFiles" |sed 's!.*/!!' | sed 's/_ca.bam//g' | sed 's/.bam//g' | xargs echo); echo $bamLabels
+if [ $# -e 1 ]; then
+    bamFiles=$(find $bamDir | grep ".bam$" | grep -v "unmapped" | sort)
+else
+    bamFiles=$*
+fi
+
+bamLabels=$(echo "$bamFiles" | xargs -n1 basename | sed 's!.*/!!' | sed 's/_mmf.bam//g' |  sed 's/_ca.bam//g' | sed 's/.bam//g' | xargs echo); echo $bamLabels
+
 
 ## see how well bam files correlate using untrimmed data
 bcCmd="bamCorrelate bins --bamfiles $(echo $bamFiles | xargs echo) --labels $bamLabels --plotFile='bc.pdf' --outFileCorMatrix='bc.txt' --numberOfProcessors=6 --corMethod spearman --zMin 0.5 --zMax 1"
-mysub "${project}__bamcorrelate" "$bcCmd"  -q long -n 4 -R span[hosts=1] | blockScript .bamcorrelate
-
-mailme "$project: bamcorrelate done in $(pwd)"
+echo $bcCmd
+#mysub "${project}__bamcorrelate" "$bcCmd"  -q long -n 4 -R span[hosts=1] | blockScript .bamcorrelate
+#mailme "$project: bamcorrelate done in $(pwd)"
 
 }
 export -f dge_bam_correlate