Mercurial > repos > bioitcore > splicetrap

comparison bin/vslz.pl @ 1:adc0f7765d85 draft

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planemo upload
author bioitcore
date Thu, 07 Sep 2017 15:06:58 -0400
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0:d4ca551ca300 1:adc0f7765d85
1 use strict;
2 exit;
3
4 my %config=do "$ENV{HOME}/.SpliceTrap.pl.ini";
5 my $SrcFolder=$config{SrcFolder};
6
7 my $BedFileName=$SrcFolder."/db/TXdb.1101.bed";
8 my $RatioFileName=$ARGV[0];
9 my $BedFileOutName=$ARGV[1];
10 my %Ratios;
11
12 open(RatioFile, $RatioFileName);
13
14 while(my $RatioLine=<RatioFile>)
15 {
16 chomp($RatioLine);
17 my @array=split("\t",$RatioLine);
18 $Ratios{$array[0]}=$array[2] if $array[14] eq "passed";
19 }
20
21 close(RatioFile);
22
23 open(BedFile, $BedFileName);
24 open(BedFileOut,">".$BedFileOutName.".bed");
25 print BedFileOut "track name=$BedFileOutName discription=$BedFileOutName useScore=1\n";
26 while(my $BedLine=<BedFile>)
27 {
28 my @array=split("\t",$BedLine);
29 $array[3]=~/^(\S*)\[([LS])\]/;
30 my $id=$1;
31 my $LS=$2;
32 #print $LS,"\n";
33 next if not exists $Ratios{$id};
34 $array[4]=$Ratios{$id};
35 $array[4]=1-$Ratios{$id} if( $LS eq 'S');
36
37 $array[4]=sprintf("%.0f",$array[4]*1000);
38 for (my $i=0;$i<@array; $i++)
39 {
40 print BedFileOut $array[$i];
41 print BedFileOut "\t" if $i<scalar(@array)-1;
42 }
43 #print BedFileOut "\n";
44 }
45 close(BedFileOut);
46 close(BedFile);