--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NEUMA-1.2.1/iNIR2iFVKM.pl	Thu Aug 08 00:46:13 2013 -0400
@@ -0,0 +1,35 @@
+#!/usr/bin/perl
+
+if(@ARGV<2) { print "usage: $0 iNIR_file iEUMA_file > output.iFVKM\n"; exit; }
+my ($iNIR_file,$iEUMA_file) = @ARGV;
+
+open IN, $iNIR_file or die "Can't open iNIR_file $sample_iNIR_file\n";
+<IN>;  # skip header
+while(<IN>){
+  chomp;
+  split/\t/;
+  $gene = $_[0]."\t".$_[1];
+  $RNAseq{$gene}=$_[2];
+}
+close IN;
+
+open IN, $iEUMA_file or die "Can't open iEUMA file $iEUMA_file\n";
+while(<IN>){
+  chomp;
+  split/\t/;
+  $gene = $_[0]."\t".$_[1];
+  $iEUMA{$gene}=$_[2];
+}
+close IN;
+
+
+print "gene\tisoform\tiFVK\tread.count\tiEUMA(bp)\n";
+for my $gene (sort keys %iEUMA){
+ next if $iEUMA{$gene} ==0;
+ if(!exists $RNAseq{$gene}){ $RNAseq{$gene} = 0; }
+ my $iFVKM = $RNAseq{$gene} / $iEUMA{$gene} * 1000;
+ print "$gene\t$iFVKM\t$RNAseq{$gene}\t$iEUMA{$gene}\n";
+}
+
+
+