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comparison NEUMA-1.2.1/iNIR2iFVKM.pl @ 0:c44c43d185ef draft default tip

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NEUMA-1.2.1 Uploaded
author chawhwa
date Thu, 08 Aug 2013 00:46:13 -0400
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-1:000000000000 0:c44c43d185ef
1 #!/usr/bin/perl
2
3 if(@ARGV<2) { print "usage: $0 iNIR_file iEUMA_file > output.iFVKM\n"; exit; }
4 my ($iNIR_file,$iEUMA_file) = @ARGV;
5
6 open IN, $iNIR_file or die "Can't open iNIR_file $sample_iNIR_file\n";
7 <IN>; # skip header
8 while(<IN>){
9 chomp;
10 split/\t/;
11 $gene = $_[0]."\t".$_[1];
12 $RNAseq{$gene}=$_[2];
13 }
14 close IN;
15
16 open IN, $iEUMA_file or die "Can't open iEUMA file $iEUMA_file\n";
17 while(<IN>){
18 chomp;
19 split/\t/;
20 $gene = $_[0]."\t".$_[1];
21 $iEUMA{$gene}=$_[2];
22 }
23 close IN;
24
25
26 print "gene\tisoform\tiFVK\tread.count\tiEUMA(bp)\n";
27 for my $gene (sort keys %iEUMA){
28 next if $iEUMA{$gene} ==0;
29 if(!exists $RNAseq{$gene}){ $RNAseq{$gene} = 0; }
30 my $iFVKM = $RNAseq{$gene} / $iEUMA{$gene} * 1000;
31 print "$gene\t$iFVKM\t$RNAseq{$gene}\t$iEUMA{$gene}\n";
32 }
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