Mercurial > repos > bioitcore > splicetrap
view PostAnalysis @ 5:2ebca9da5e42 draft default tip
planemo upload
author | bioitcore |
---|---|
date | Thu, 07 Sep 2017 17:39:24 -0400 |
parents | adc0f7765d85 |
children |
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#!/usr/bin/perl my $SrcFolder="/home/galaxy/galaxy-dist/tools/SpliceTrap.0.90.1/bin"; # this script is a wrapup for Post analysis based on the ratio file output use strict; use Getopt::Long; my $RatioFile=""; my $OutputFile = ""; my $JunctionCut=5; my $CutoffLevel="M"; my $noIRM = 0; my $noIRMstr=""; GetOptions ( "i:s"=>\$RatioFile, "o:s"=>\$OutputFile, "c:s"=>\$CutoffLevel, "noIRM|noirm"=>\$noIRM, "j:i"=>\$JunctionCut ); my $InputParaDes=" Usage of the script: -i input file (.ratio file) -o output file -c Cutoff Level:H/[M]/L Means High, Middle or Low -j Junction reads per junction requirement for each exon-isoform [5] --noIRM Use the unadjusted inclusion ratios (before IRM correction) "; if($RatioFile eq "") { print $InputParaDes; exit; } if($CutoffLevel ne "H" and $CutoffLevel ne "M" and $CutoffLevel ne "L") { print $InputParaDes; exit; } if($noIRM) { $noIRMstr= "noirm"; } system("perl $SrcFolder/ApplyCutoff.jie.pl $RatioFile $CutoffLevel $JunctionCut $noIRMstr >$OutputFile.raw"); open(rawfile, "$OutputFile.raw"); open(outfile, ">$OutputFile"); while(my $line=<rawfile>) { chomp($line); my @a=split("\t",$line); if($noIRM) { print outfile join("\t",$a[21],$a[1],$a[3],$a[4],$a[5],$a[6],$a[7],$a[11],$a[12],$a[13],$a[14]),"\n"; } else { print outfile join("\t",$a[21],$a[2],$a[3],$a[4],$a[5],$a[6],$a[7],$a[11],$a[12],$a[13],$a[14]),"\n"; } } close(outfile); close(rawfile);