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comparison bin/PostAnalysis.pl @ 1:adc0f7765d85 draft

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