Mercurial > repos > kyost > atac_primer_tool

annotate window_coverage.bash @ 4:72571a30f17b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Add test for unique peak names.
author kyost
date Wed, 02 May 2018 13:20:21 -0400
parents fd3ea97a96bc
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
1 #!/bin/bash
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
2
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
3 #Requires bam files and bed file containing coordinates of peaks of interest
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
4 #Determines regions within peaks where included fragement coverage best correlates
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
5 #with total read count under peak. Exports regions as bed file.
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
6
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
7 #required arguements:
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
8 #($1): series of bam files
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
9 #($2): file names of bam files
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
10 #($3): window bed file
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
11 #($4): percent of window fragments must cover, default is 0.9
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
12 #($5): output coverage file
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
13 #($6): output spanning fragment coverage file
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
14
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
15 #Usage: ATAC_qPCR_regions.bash bam_series name_list qPCR_windows.bed 0.9 combined.o.bed.coverage combined.f9.bed.coverage
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
16
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
17 bam_series=$1
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
18 name_list=$2
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
19 qPCR_windows=$3
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
20 percent_overlap=${4:-0.9}
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
21 combined_o=$5
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
22 combined_f9=$6
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
23
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
24 COUNTER=0
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
25 echo $bam_series |tr , '\n' > bam_series.txt
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
26 echo $name_list | tr , '\n' > name_list.txt
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
27 paste name_list.txt bam_series.txt > bam_name_list.txt
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
28 sort -k1 bam_name_list.txt > sorted_bam_name_list.txt
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
29 cut -f 2 sorted_bam_name_list.txt > sorted_bam_list.txt
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
30
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
31 cat sorted_bam_list.txt | while read file
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
32 do
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
33
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
34 #create bed file of fragments for each bam file
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
35
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
36 samtools sort -n -o - $file | samtools fixmate - - | bamToBed -i - -bedpe | cut -f 1,2,6 > "${file}".includeinsert.bed
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
37
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
38 #determine window coverage for each bam file
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
39 #combined_o: Total reads in peak/window
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
40 #combined_f9: Spanning reads in window
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
41
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
42 if [ $COUNTER -eq 0 ]
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
43 then
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
44 coverageBed -a $qPCR_windows -b $file | cut -f 1,2,3,4,5 > $combined_o
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
45 coverageBed -a $qPCR_windows -b "${file}".includeinsert.bed -f $percent_overlap | cut -f 1,2,3,4,5 > $combined_f9
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
46
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
47 else
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
48 coverageBed -a $qPCR_windows -b $file | cut -f 5 > temp.o.bed.coverage
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
49 coverageBed -a $qPCR_windows -b "${file}".includeinsert.bed -f $percent_overlap | cut -f 5 > temp.f9.bed.coverage
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
50 paste $combined_o temp.o.bed.coverage > combined.temp.o.bed.coverage
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
51 mv combined.temp.o.bed.coverage $combined_o
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
52 paste $combined_f9 temp.f9.bed.coverage > combined.temp.f9.bed.coverage
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
53 mv combined.temp.f9.bed.coverage $combined_f9
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
54
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
55 rm temp.o.bed.coverage
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
56 rm temp.f9.bed.coverage
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
57
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
58 fi
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
59
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
60 rm "${file}.includeinsert.bed"
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
61
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
62 let COUNTER=COUNTER+1
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
63
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
64 done
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
65
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
66
fd3ea97a96bc planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
kyost
parents:
diff changeset
67 rm *.txt