From 63b17d41d4ed655a7a45bf9d5cb3bf3f84789809 Mon Sep 17 00:00:00 2001
From: Holger Brandl <holgerbrandl@gmail.com>
Date: Thu, 17 Sep 2015 14:46:36 +0200
Subject: [PATCH] more flexible bam correlation wrapper
---
dge_workflow/dge_utils.sh | 22 +++++++++++++++-------
1 file changed, 15 insertions(+), 7 deletions(-)
diff --git a/dge_workflow/dge_utils.sh b/dge_workflow/dge_utils.sh
index b67c65a..38e4285 100755
--- a/dge_workflow/dge_utils.sh
+++ b/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
--
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