Mercurial > repos > kyost > atac_primer_tool

comparison window_coverage.bash @ 0:fd3ea97a96bc draft

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planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
author kyost
date Sat, 28 Apr 2018 15:07:26 -0400
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-1:000000000000 0:fd3ea97a96bc
1 #!/bin/bash
2
3 #Requires bam files and bed file containing coordinates of peaks of interest
4 #Determines regions within peaks where included fragement coverage best correlates
5 #with total read count under peak. Exports regions as bed file.
6
7 #required arguements:
8 #($1): series of bam files
9 #($2): file names of bam files
10 #($3): window bed file
11 #($4): percent of window fragments must cover, default is 0.9
12 #($5): output coverage file
13 #($6): output spanning fragment coverage file
14
15 #Usage: ATAC_qPCR_regions.bash bam_series name_list qPCR_windows.bed 0.9 combined.o.bed.coverage combined.f9.bed.coverage
16
17 bam_series=$1
18 name_list=$2
19 qPCR_windows=$3
20 percent_overlap=${4:-0.9}
21 combined_o=$5
22 combined_f9=$6
23
24 COUNTER=0
25 echo $bam_series |tr , '\n' > bam_series.txt
26 echo $name_list | tr , '\n' > name_list.txt
27 paste name_list.txt bam_series.txt > bam_name_list.txt
28 sort -k1 bam_name_list.txt > sorted_bam_name_list.txt
29 cut -f 2 sorted_bam_name_list.txt > sorted_bam_list.txt
30
31 cat sorted_bam_list.txt | while read file
32 do
33
34 #create bed file of fragments for each bam file
35
36 samtools sort -n -o - $file | samtools fixmate - - | bamToBed -i - -bedpe | cut -f 1,2,6 > "${file}".includeinsert.bed
37
38 #determine window coverage for each bam file
39 #combined_o: Total reads in peak/window
40 #combined_f9: Spanning reads in window
41
42 if [ $COUNTER -eq 0 ]
43 then
44 coverageBed -a $qPCR_windows -b $file | cut -f 1,2,3,4,5 > $combined_o
45 coverageBed -a $qPCR_windows -b "${file}".includeinsert.bed -f $percent_overlap | cut -f 1,2,3,4,5 > $combined_f9
46
47 else
48 coverageBed -a $qPCR_windows -b $file | cut -f 5 > temp.o.bed.coverage
49 coverageBed -a $qPCR_windows -b "${file}".includeinsert.bed -f $percent_overlap | cut -f 5 > temp.f9.bed.coverage
50 paste $combined_o temp.o.bed.coverage > combined.temp.o.bed.coverage
51 mv combined.temp.o.bed.coverage $combined_o
52 paste $combined_f9 temp.f9.bed.coverage > combined.temp.f9.bed.coverage
53 mv combined.temp.f9.bed.coverage $combined_f9
54
55 rm temp.o.bed.coverage
56 rm temp.f9.bed.coverage
57
58 fi
59
60 rm "${file}.includeinsert.bed"
61
62 let COUNTER=COUNTER+1
63
64 done
65
66
67 rm *.txt