|
0
|
1 #!/bin/bash
|
|
|
2
|
|
|
3 #sub1.chr22_21349676-21349677.sample02.bam
|
|
|
4
|
|
|
5 bam=$1;
|
|
|
6 name=$(echo $bam | cut -d'.' -f1)
|
|
|
7 region=$(echo $bam | cut -d'.' -f2)
|
|
|
8 sample=$(echo $bam | cut -d'.' -f3)
|
|
|
9
|
|
|
10 chr=$(echo $region | cut -d'_' -f1)
|
|
|
11 pos=$(echo $region | cut -d'_' -f2)
|
|
|
12
|
|
|
13 beg=$(echo $pos | cut -d'-' -f1)
|
|
|
14 end=$(echo $pos | cut -d'-' -f2)
|
|
|
15
|
|
|
16 #beg=$(($beg+50))
|
|
|
17 #end=$((end-50))
|
|
|
18
|
|
|
19 #echo "name $name"
|
|
|
20 #echo "region $region"
|
|
|
21 #echo "sample $sample"
|
|
|
22
|
|
|
23 echo "$name $chr:$beg-$end $sample"
|
|
|
24 echo "$name $chr:$beg-$end $sample" >> MACARON_validate.txt
|
|
|
25
|
|
|
26 samtools view $bam | awk -v start=$beg -v stop=$end '
|
|
|
27 {
|
|
|
28 pos=$4;
|
|
|
29 if(pos < start){
|
|
|
30 cstart=1+start-pos;
|
|
|
31 cstop=1+stop-pos;
|
|
|
32 print cstart"."cstop"."$10;
|
|
|
33 }
|
|
|
34 }' > tmp
|
|
|
35
|
|
|
36 while read line;
|
|
|
37 do
|
|
|
38 cb=$(echo $line | cut -d'.' -f1);
|
|
|
39 ce=$(echo $line | cut -d'.' -f2);
|
|
|
40 seq=$(echo $line | cut -d'.' -f3);
|
|
|
41 echo $seq | cut -c$cb-$ce;
|
|
|
42 done <tmp | sort | uniq -c | sort -n >> MACARON_validate.txt
|
|
|
43 rm tmp
|
|
|
44
|
|
|
45
|
|
|
46
|
|
|
47
|
|
|
48 exit 0
|
|
|
49
|
