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comparison JunctionDiff-vs-background.sh @ 0:1209f18a5a83 draft

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author saskia-hiltemann
date Mon, 03 Aug 2015 05:01:15 -0400
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children 885ba15c2564
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-1:000000000000 0:1209f18a5a83
1 #!/bin/bash
2
3 #JunctionDiff-vs-background.sh $variants $genomes ${reference.fields.crr_path} ${reference.fields.31G_var_paths} ${reference.54G_var_paths} $output_filtered $output_report $scoreThresholdA $scoreThresholdB $distance $minlength
4
5 #set some defaults
6 output_report="output_reports.tsv"
7
8 set -- `getopt -n$0 -u -a --longoptions="variants: reference: VN_junctions: cgatools_binary: outputfile_filtered: outputfile_report: scoreThresholdA: scoreThresholdB: distance: minlength: " "h:" "$@"` || usage
9 [ $# -eq 0 ] && usage
10
11 while [ $# -gt 0 ]
12 do
13 case "$1" in
14 --variants) variants=$2;shift;;
15 --reference) crr=$2;shift;;
16 --VN_junctions) VN_junctionfiles_list=$2;shift;;
17 --cgatools_binary) cgatools_binary=$2;shift;; #cgatools binary to use
18 --outputfile_filtered) output_filtered=$2;shift;;
19 --outputfile_report) output_report=$2;shift;;
20 --scoreThresholdA) scoreThresholdA=$2;shift;;
21 --scoreThresholdB) scoreThresholdB=$2;shift;;
22 --distance) distance=$2;shift;;
23 --minlength) minlength=$2;shift;;
24 -h) shift;;
25 --) shift;break;;
26 -*) usage;;
27 *) break;;
28 esac
29 shift
30 done
31
32
33 # make copy of input junctions file, as this file will be altered
34 junctions="junctions.tsv"
35 cp $variants $junctions
36
37
38 ### run JunctionDiff against all of the VN junctionfiles
39
40 echo "running JunctionDiff against each of the VN genomes"
41
42 # for each line in VN genomes list of junctionfiles, run junctiondiff
43 count=0
44 while read line
45 do
46 if [[ $line != "" ]] # catch empty lines
47 then
48 count=$[$count+1]
49 ${cgatools_binary} junctiondiff \
50 --beta \
51 --statout \
52 --reference $crr \
53 --junctionsA $junctions \
54 --junctionsB $line \
55 --scoreThresholdA $scoreThresholdA \
56 --scoreThresholdB $scoreThresholdB \
57 --distance $distance \
58 --minlength $minlength
59
60 #concatenate all reports
61 echo -e "report of run $count:\n----------------------" >> $output_report
62 cat report.tsv >> $output_report
63 echo "" >> $output_report
64
65
66 #rename output file to junctions file for next iteration
67 rm $junctions
68 mv "diff-$junctions" $junctions
69 fi
70 done < $VN_junctionfiles_list
71
72 cp $junctions $output_filtered
73
74
75