Mercurial > repos > jbrayet > controlsubset_1_0_docker
changeset 0:3b1e9f048405 draft
Uploaded
| author | jbrayet |
|---|---|
| date | Tue, 02 Feb 2016 09:02:11 -0500 |
| parents | |
| children | d9fb544723cb |
| files | createControlSubSet_wrapper.sh |
| diffstat | 1 files changed, 48 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/createControlSubSet_wrapper.sh Tue Feb 02 09:02:11 2016 -0500 @@ -0,0 +1,48 @@ +#!/bin/bash + +CONTROLFILE="" + +while getopts "f:c:t:o:s:q:p:" optionName; do +case "$optionName" in + +f) CHIPFILE="$OPTARG";; +c) CONTROLFILE="$OPTARG";; +t) TYPE="$OPTARG";; +s) CHIPOUTPUT="$OPTARG";; +o) CONTROLOUTPUT="$OPTARG";; +q) IFPROCSAMPLE="$OPTARG";; +p) IFOUTSAM="$OPTARG";; + +esac +done + +local_path=/usr/bin/controlsubset + +LOGTMP=$IFOUTSAM.log.tmp + +if [[ $IFPROCSAMPLE == "Yes" ]] + then + perl $local_path/createControlSubSet.pl -f $CHIPFILE -c $CONTROLFILE -t $TYPE -s $CHIPOUTPUT -o $CONTROLOUTPUT >$LOGTMP 2>>$LOGTMP +else + perl $local_path/createControlSubSet.pl -f $CHIPFILE -c $CONTROLFILE -t $TYPE -o $CONTROLOUTPUT >>$LOGTMP 2>>$LOGTMP +fi + +if [[ $TYPE == "bam" && $IFOUTSAM == "No" ]] + then + + samtools view -S -b $CONTROLOUTPUT 2>>$LOGTMP | samtools sort -m 4000000000 - $CONTROLOUTPUT 2>>$LOGTMP + rm $CONTROLOUTPUT + mv $CONTROLOUTPUT.bam $CONTROLOUTPUT + + if [[ $IFPROCSAMPLE == "Yes" ]] + then + samtools view -S -b $CHIPOUTPUT 2>>$LOGTMP | samtools sort -m 4000000000 - $CHIPOUTPUT 2>>$LOGTMP + rm $CHIPOUTPUT + mv $CHIPOUTPUT.bam $CHIPOUTPUT + fi +fi + +head -2 $LOGTMP +if [ -r $LOGTMP ]; then + rm $LOGTMP +fi