Mercurial > repos > jbrayet > controlsubset_1_0_docker
comparison createControlSubSet_wrapper.sh @ 0:3b1e9f048405 draft
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author | jbrayet |
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date | Tue, 02 Feb 2016 09:02:11 -0500 |
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-1:000000000000 | 0:3b1e9f048405 |
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1 #!/bin/bash | |
2 | |
3 CONTROLFILE="" | |
4 | |
5 while getopts "f:c:t:o:s:q:p:" optionName; do | |
6 case "$optionName" in | |
7 | |
8 f) CHIPFILE="$OPTARG";; | |
9 c) CONTROLFILE="$OPTARG";; | |
10 t) TYPE="$OPTARG";; | |
11 s) CHIPOUTPUT="$OPTARG";; | |
12 o) CONTROLOUTPUT="$OPTARG";; | |
13 q) IFPROCSAMPLE="$OPTARG";; | |
14 p) IFOUTSAM="$OPTARG";; | |
15 | |
16 esac | |
17 done | |
18 | |
19 local_path=/usr/bin/controlsubset | |
20 | |
21 LOGTMP=$IFOUTSAM.log.tmp | |
22 | |
23 if [[ $IFPROCSAMPLE == "Yes" ]] | |
24 then | |
25 perl $local_path/createControlSubSet.pl -f $CHIPFILE -c $CONTROLFILE -t $TYPE -s $CHIPOUTPUT -o $CONTROLOUTPUT >$LOGTMP 2>>$LOGTMP | |
26 else | |
27 perl $local_path/createControlSubSet.pl -f $CHIPFILE -c $CONTROLFILE -t $TYPE -o $CONTROLOUTPUT >>$LOGTMP 2>>$LOGTMP | |
28 fi | |
29 | |
30 if [[ $TYPE == "bam" && $IFOUTSAM == "No" ]] | |
31 then | |
32 | |
33 samtools view -S -b $CONTROLOUTPUT 2>>$LOGTMP | samtools sort -m 4000000000 - $CONTROLOUTPUT 2>>$LOGTMP | |
34 rm $CONTROLOUTPUT | |
35 mv $CONTROLOUTPUT.bam $CONTROLOUTPUT | |
36 | |
37 if [[ $IFPROCSAMPLE == "Yes" ]] | |
38 then | |
39 samtools view -S -b $CHIPOUTPUT 2>>$LOGTMP | samtools sort -m 4000000000 - $CHIPOUTPUT 2>>$LOGTMP | |
40 rm $CHIPOUTPUT | |
41 mv $CHIPOUTPUT.bam $CHIPOUTPUT | |
42 fi | |
43 fi | |
44 | |
45 head -2 $LOGTMP | |
46 if [ -r $LOGTMP ]; then | |
47 rm $LOGTMP | |
48 fi |