comparison bin/PostAnalysis @ 1:adc0f7765d85 draft

planemo upload
author bioitcore
date Thu, 07 Sep 2017 15:06:58 -0400
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0:d4ca551ca300 1:adc0f7765d85
1 #!/usr/bin/perl
2 my $SrcFolder="/home/galaxy/galaxy-dist/tools/SpliceTrap.0.90.1/bin";
3 # this script is a wrapup for Post analysis based on the ratio file output
4
5 use strict;
6 use Getopt::Long;
7 my $RatioFile="";
8 my $OutputFile = "";
9 my $JunctionCut=5;
10 my $CutoffLevel="M";
11 my $noIRM = 0;
12 my $noIRMstr="";
13
14 GetOptions (
15 "i:s"=>\$RatioFile,
16 "o:s"=>\$OutputFile,
17 "c:s"=>\$CutoffLevel,
18 "noIRM|noirm"=>\$noIRM,
19 "j:i"=>\$JunctionCut
20 );
21
22 my $InputParaDes=" Usage of the script:
23 -i input file (.ratio file)
24 -o output file
25 -c Cutoff Level:H/[M]/L
26 Means High, Middle or Low
27 -j Junction reads per junction requirement for each exon-isoform [5]
28 --noIRM Use the unadjusted inclusion ratios (before IRM correction)
29 ";
30
31 if($RatioFile eq "")
32 {
33 print $InputParaDes;
34 exit;
35 }
36
37 if($CutoffLevel ne "H" and $CutoffLevel ne "M" and $CutoffLevel ne "L")
38 {
39 print $InputParaDes;
40 exit;
41 }
42 if($noIRM)
43 {
44 $noIRMstr= "noirm";
45 }
46
47
48 system("perl $SrcFolder/ApplyCutoff.jie.pl $RatioFile $CutoffLevel $JunctionCut $noIRMstr >$OutputFile.raw");
49
50 open(rawfile, "$OutputFile.raw");
51 open(outfile, ">$OutputFile");
52 while(my $line=<rawfile>)
53 {
54 chomp($line);
55 my @a=split("\t",$line);
56 if($noIRM)
57 {
58 print outfile join("\t",$a[21],$a[1],$a[3],$a[4],$a[5],$a[6],$a[7],$a[11],$a[12],$a[13],$a[14]),"\n";
59 }
60 else
61 {
62 print outfile join("\t",$a[21],$a[2],$a[3],$a[4],$a[5],$a[6],$a[7],$a[11],$a[12],$a[13],$a[14]),"\n";
63 }
64 }
65 close(outfile);
66 close(rawfile);