1
1
#! /usr/bin/env bash
2
+ set -x
2
3
3
- # #!/bin/sh -x
4
4
5
5
index=' hg19'
6
6
mapq=0
7
-
8
- # find pattern of base files NOT
9
- # bam replaced with .pre_ltr.bowtie2.hg19.bam
10
- # and .post_ltr.bowtie2.hg19.bam
11
- base=' bowtie2.herv_k113_ltr_ends.__very_sensitive_local.aligned'
7
+ core=' bowtie2.herv_k113_ltr_ends.__very_sensitive_local.aligned'
12
8
basedir=` pwd`
13
9
10
+
14
11
function usage(){
15
12
echo
16
13
echo " Usage: (NO EQUALS SIGNS)"
17
14
echo
18
15
echo " ` basename $0 ` "
19
16
echo
20
- echo " ` basename $0 ` [--index STRING] [--mapq INTEGER] [--base 'STRING'] sampledir(s)"
17
+ echo " ` basename $0 ` [--index STRING] [--mapq INTEGER] [--core 'STRING'] sampledir(s)"
21
18
echo
22
19
echo " Example:"
23
20
echo " ` basename $0 ` NA211??"
@@ -26,7 +23,7 @@ function usage(){
26
23
echo " Defaults:"
27
24
echo " --index/-i .. : $index "
28
25
echo " --mapq/-q .. : $mapq "
29
- echo " --base/-b ... : $base "
26
+ echo " --core/-c ... : $core "
30
27
echo
31
28
echo " Output directed to file, similarly named."
32
29
echo
@@ -39,8 +36,8 @@ while [ $# -ne 0 ] ; do
39
36
shift ; index=$1 ; shift ;;
40
37
-q|--mapq* )
41
38
shift ; mapq=$1 ; shift ;;
42
- -b |--b * )
43
- shift ; base =$1 ; shift ;;
39
+ -c |--c * )
40
+ shift ; core =$1 ; shift ;;
44
41
-* )
45
42
echo ; echo " Unexpected args from: ${* } " ; usage ;;
46
43
* )
@@ -61,13 +58,12 @@ logfile=`basename $0`.$index.$quality.$date.out
61
58
echo " index : $index "
62
59
echo " mapq : $mapq "
63
60
echo " quality : $quality "
64
- echo " base : $base "
61
+ echo " core : $core "
65
62
echo
66
63
67
64
# TCGA-41-5651-01A.bowtie2.herv_k113_ltr_ends.__very_sensitive_local.aligned.bam
68
65
69
66
while [ $# -ne 0 ] ; do
70
- # for bam in `find . -depth 2 -name $findpattern`; do
71
67
cd $basedir
72
68
73
69
# echo $bam
@@ -85,7 +81,7 @@ logfile=`basename $0`.$index.$quality.$date.out
85
81
# echo $base
86
82
# TCGA-02-2483-01A.bowtie2.herv_k113_ltr_ends.__very_sensitive_local.aligned.bam
87
83
88
- echo $base
84
+ echo $core
89
85
# *bowtie2.herv_k113_ltr_ends.__very_sensitive_local.aligned
90
86
91
87
# base=${base%.*} # drop the extension
@@ -97,23 +93,23 @@ logfile=`basename $0`.$index.$quality.$date.out
97
93
98
94
# TCGA-41-5651-01A.bowtie2.herv_k113_ltr_ends.__very_sensitive_local.aligned.pre_ltr.bowtie2.hg19.bam
99
95
100
- samtools view -q $mapq -F 20 $sample .$base .pre_ltr.bowtie2.$index .bam \
96
+ samtools view -q $mapq -F 20 $sample .$core .pre_ltr.bowtie2.$index .bam \
101
97
| awk ' {print $3":"$4+length($10)}' \
102
- | sort > $sample .$base .pre_ltr.bowtie2.$index .$quality .insertion_points
103
- samtools view -q $mapq -F 20 $sample .$base .post_ltr.bowtie2.$index .bam \
98
+ | sort > $sample .$core .pre_ltr.bowtie2.$index .$quality .insertion_points
99
+ samtools view -q $mapq -F 20 $sample .$core .post_ltr.bowtie2.$index .bam \
104
100
| awk ' {print $3":"$4}' \
105
- | sort > $sample .$base .post_ltr.bowtie2.$index .$quality .insertion_points
106
- positions_within_10bp.sh $sample .$base .* .bowtie2.$index .$quality .insertion_points \
107
- | sort | uniq -c > $sample .$base .both_ltr.bowtie2.$index .$quality .insertion_points.overlappers
101
+ | sort > $sample .$core .post_ltr.bowtie2.$index .$quality .insertion_points
102
+ positions_within_10bp.sh $sample .$core .* .bowtie2.$index .$quality .insertion_points \
103
+ | sort | uniq -c > $sample .$core .both_ltr.bowtie2.$index .$quality .insertion_points.overlappers
108
104
109
- samtools view -q $mapq -F 4 -f 16 $sample .$base .pre_ltr.bowtie2.$index .bam \
105
+ samtools view -q $mapq -F 4 -f 16 $sample .$core .pre_ltr.bowtie2.$index .bam \
110
106
| awk ' {print $3":"$4}' \
111
- | sort > $sample .$base .pre_ltr.bowtie2.$index .$quality .rc_insertion_points
112
- samtools view -q $mapq -F 4 -f 16 $sample .$base .post_ltr.bowtie2.$index .bam \
107
+ | sort > $sample .$core .pre_ltr.bowtie2.$index .$quality .rc_insertion_points
108
+ samtools view -q $mapq -F 4 -f 16 $sample .$core .post_ltr.bowtie2.$index .bam \
113
109
| awk ' {print $3":"$4+length($10)}' \
114
- | sort > $sample .$base .post_ltr.bowtie2.$index .$quality .rc_insertion_points
115
- positions_within_10bp.sh $sample .$base .* .bowtie2.$index .$quality .rc_insertion_points \
116
- | sort | uniq -c > $sample .$base .both_ltr.bowtie2.$index .$quality .rc_insertion_points.rc_overlappers
110
+ | sort > $sample .$core .post_ltr.bowtie2.$index .$quality .rc_insertion_points
111
+ positions_within_10bp.sh $sample .$core .* .bowtie2.$index .$quality .rc_insertion_points \
112
+ | sort | uniq -c > $sample .$core .both_ltr.bowtie2.$index .$quality .rc_insertion_points.rc_overlappers
117
113
118
114
shift
119
115
done
0 commit comments