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comparison NEUMA-1.2.1/gNIR2gFVKM.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: $0 gNIR_file EUMA_file > output.gFVKM\n"; exit; }
4 my ($gNIR_file,$EUMA_file) = @ARGV;
5
6 open IN, $gNIR_file or die "Can't open gNIR_file $gNIR_file\n";
7 <IN>; # skip header
8 while(<IN>){
9 chomp;
10 split/\t/;
11 $RNAseq{$_[0]}=$_[1];
12 }
13 close IN;
14
15 open IN, $EUMA_file or die "Can't open EUMA file $EUMA_file\n";
16 while(<IN>){
17 chomp;
18 split/\t/;
19 $EUMA{$_[0]}=$_[1];
20 }
21 close IN;
22
23
24 print "gene\tgFVK\tread.count\tgEUMA(bp)\n";
25 for my $gene (sort keys %EUMA){
26 next if $EUMA{$gene} ==0;
27 if(!exists $RNAseq{$gene}){ $RNAseq{$gene} = 0; }
28 $gFVKM = $RNAseq{$gene} / $EUMA{$gene} * 1000;
29 print "$gene\t$gFVKM\t$RNAseq{$gene}\t$EUMA{$gene}\n";
30 }
31
32