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comparison NEUMA-1.2.1/merge_LVKM.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<4) { print "usage: $0 genewise/isoformwise[g/i] EUMAcut LVKM_out_dir NR(1/0) > output.gLVKM(iLVKM).merged\n"; exit; }
4 my $option = shift @ARGV; #either g or i
5 my $EUMAcut = shift @ARGV;
6 my $LVKM_dir = shift @ARGV;
7 my $NR_option = shift @ARGV;
8
9 my $suffix = $option."LVKM";
10
11 my @sample_list = split/\n/,`ls -1 $LVKM_dir`;
12 for my $i (0..$#sample_list){
13 if($NR_option eq '1'){
14 if($sample_list[$i] =~ /\.\d+.-NR.[gi]LVKM$/) { $samples{$`}=1; }
15 }
16 else {
17 if($sample_list[$i] =~ /\.\d+.[gi]LVKM$/) { $samples{$`}=1; }
18 }
19 }
20
21 @sample_list = keys %samples;
22
23
24 for my $sample (@sample_list){
25 next if($sample eq '');
26 my $file;
27 if($NR_option eq '1'){
28 $file = "$LVKM_dir/$sample.$EUMAcut.-NR.$suffix";
29 }
30 else {
31 $file = "$LVKM_dir/$sample.$EUMAcut.$suffix";
32 }
33
34 print STDERR "$file\n"; #DEBUGGING
35 open IN,$file or die "Can't open LVKM file $file\n";
36 <IN>;
37 while(<IN>){
38 chomp;
39
40 my $gene;
41 if($option eq 'g'){
42 my ($gid,$symbol,$expr) = (split/\t/)[0,1,2];
43 $gene = "$gid\t$symbol";
44 $EXPR{$gene}{$sample} = $expr;
45 }
46 elsif($option eq 'i'){
47 my ($gid,$symbol,$NM,$expr) = (split/\t/)[0,1,2,3];
48 $gene = "$gid\t$symbol\t$NM";
49 $EXPR{$gene}{$sample} = $expr;
50 }
51 }
52 close IN;
53 }
54
55
56
57 $"="\t";
58 if($option eq 'g') { print "gene.id\tgene.symbol\t@sample_list\n"; }
59 elsif($option eq 'i') { print "gene.id\tgene.symbol\tisoform\t@sample_list\n"; }
60 for my $gene (keys %EXPR){
61 print "$gene";
62 for my $sample (@sample_list){
63 if(exists ${$EXPR{$gene}}{$sample}){
64 print "\t$EXPR{$gene}{$sample}";
65 }
66 else { print "\tNA"; }
67 }
68 print "\n";
69 }
70
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72