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planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
author kyost
date Fri, 04 May 2018 02:24:47 -0400
parents fd3ea97a96bc
children
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1 #!/bin/bash
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2
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3 #Requires bam files and bed file containing coordinates of peaks of interest
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4 #Determines regions within peaks where included fragement coverage best correlates
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5 #with total read count under peak. Exports regions as bed file.
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6
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7 #required arguements:
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8 #($1): series of bam files
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9 #($2): file names of bam files
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10 #($3): window bed file
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11 #($4): percent of window fragments must cover, default is 0.9
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12 #($5): output coverage file
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13 #($6): output spanning fragment coverage file
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14
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15 #Usage: ATAC_qPCR_regions.bash bam_series name_list qPCR_windows.bed 0.9 combined.o.bed.coverage combined.f9.bed.coverage
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16
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17 bam_series=$1
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18 name_list=$2
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19 qPCR_windows=$3
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20 percent_overlap=${4:-0.9}
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21 combined_o=$5
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22 combined_f9=$6
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23
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24 COUNTER=0
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25 echo $bam_series |tr , '\n' > bam_series.txt
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26 echo $name_list | tr , '\n' > name_list.txt
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27 paste name_list.txt bam_series.txt > bam_name_list.txt
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28 sort -k1 bam_name_list.txt > sorted_bam_name_list.txt
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29 cut -f 2 sorted_bam_name_list.txt > sorted_bam_list.txt
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30
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31 cat sorted_bam_list.txt | while read file
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32 do
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33
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34 #create bed file of fragments for each bam file
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35
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36 samtools sort -n -o - $file | samtools fixmate - - | bamToBed -i - -bedpe | cut -f 1,2,6 > "${file}".includeinsert.bed
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37
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38 #determine window coverage for each bam file
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39 #combined_o: Total reads in peak/window
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40 #combined_f9: Spanning reads in window
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41
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42 if [ $COUNTER -eq 0 ]
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43 then
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44 coverageBed -a $qPCR_windows -b $file | cut -f 1,2,3,4,5 > $combined_o
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45 coverageBed -a $qPCR_windows -b "${file}".includeinsert.bed -f $percent_overlap | cut -f 1,2,3,4,5 > $combined_f9
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46
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47 else
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48 coverageBed -a $qPCR_windows -b $file | cut -f 5 > temp.o.bed.coverage
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49 coverageBed -a $qPCR_windows -b "${file}".includeinsert.bed -f $percent_overlap | cut -f 5 > temp.f9.bed.coverage
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50 paste $combined_o temp.o.bed.coverage > combined.temp.o.bed.coverage
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51 mv combined.temp.o.bed.coverage $combined_o
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52 paste $combined_f9 temp.f9.bed.coverage > combined.temp.f9.bed.coverage
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53 mv combined.temp.f9.bed.coverage $combined_f9
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54
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55 rm temp.o.bed.coverage
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56 rm temp.f9.bed.coverage
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57
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58 fi
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59
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60 rm "${file}.includeinsert.bed"
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61
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62 let COUNTER=COUNTER+1
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63
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64 done
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65
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66
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67 rm *.txt