Mercurial > repos > chawhwa > neuma

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
NEUMA-1.2.1 Uploaded
author chawhwa
date Thu, 08 Aug 2013 00:46:13 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:c44c43d185ef
1 #!/usr/bin/perl
2 # Compute gEUMA for each gene from the gUtable file and insertlendis file and print out only genes whose gEUMA is larger than 0.
3
4 if(@ARGV<3) { print "usage: $0 gUtable_file insertlendis_file READLENGTH\n"; exit; }
5
6 my ($gUtable_file,$insertlendis_file,$READLENGTH) = @ARGV;
7
8 open GUTABLE, $gUtable_file or die "Can't open gUtable file $gUtable_file\n";
9 chomp($header = <GUTABLE>);
10 @distances = split/\t/,$header;
11 shift @distances; #'gene'
12 while(<GUTABLE>){
13 chomp;
14 my @line = split/\t/;
15 my $gene = shift @line;
16 for my $i (0..$#distances){
17 $gUtable{$gene}{"$distances[$i]"}=$line[$i];
18 }
19 }
20 close GUTABLE;
21
22
23 my $totalfreq=0;
24 open LENDIS, $insertlendis_file or die "Can't open insertlendis file $insertlendis_file\n";
25 while(<LENDIS>){
26 chomp;
27 my ($insert_size, $freq) = split/\t/;
28 $insertlendis{"$insert_size"}=$freq;
29 $totalfreq+=$freq;
30 }
31 close LENDIS;
32
33 print "gene\tgEUMA\n"; #header
34 for my $gene (sort keys %gUtable){
35 my $EUMA=0;
36 for my $d (keys %{$gUtable{$gene}}){
37 $pUMA = $gUtable{$gene}{$d} * ($insertlendis{$d}/$totalfreq) ;
38 $EUMA += $pUMA;
39 }
40 if($EUMA>=0.005) { printf "$gene\t%.2f\n",$EUMA; } # use >=0.005 instead of >0, because I'm plotting two decimals after point. (in bp)
41 }
42