diff bin/PostAnalysis @ 1:adc0f7765d85 draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin/PostAnalysis	Thu Sep 07 15:06:58 2017 -0400
@@ -0,0 +1,66 @@
+#!/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);