Mercurial > repos > bioitcore > splicetrap

comparison bin/get.frag.size.pl @ 1:adc0f7765d85 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload
author bioitcore
date Thu, 07 Sep 2017 15:06:58 -0400
parents
children
comparison
equal deleted inserted replaced
0:d4ca551ca300 1:adc0f7765d85
1 #for the results from paired end
2 #The two inputs are the results from the two ends
3 use strict;
4 my $read_size = $ARGV[2];
5 open(input1, $ARGV[0]);
6 open(input2, $ARGV[1]);
7 open(output, ">$ARGV[0].fragsize");
8 #open(fusefile,">$ARGV[0].fuse");
9
10 #my $LongMarker="L";
11 #my $ShortMarker="S";
12
13 while(my $line1=<input1>)
14 {
15 my $line2=<input2>;
16 chomp($line1);
17 chomp($line2);
18 next if($line1=~/$\NM/ or $line2=~/$\NM/ or $line1=~/$\MT/ or $line2=~/$\MT/);
19 my @array1 = split("\t",$line1);
20 #my $read_size=length($array1[1]);
21 my @array2 = split("\t",$line2);
22 my $match1=$array1[3];
23 my $match2=$array2[3];
24 # my $marker=$LongMarker.$ShortMarker;
25 my @sizes=();
26 #while($match1=~/\/(\S[^,]*\[[$marker]\])\S[^,]*:(\d*)[RF]/g)
27 while($match1=~/\/(\S[^,]*\[\w+\])\S[^,]*:(\d*)[RF]/g)
28 {
29 my $name=$1;
30 my $posa=$2;
31 #print $name,"\n";
32
33 if($match2=~/\Q$name\E\S[^,]*:(\d*)[RF]/)
34 {
35 #print "match\n";
36 my $posb=$1;
37 push @sizes, abs($posb-$posa)+$read_size;
38
39 }
40
41 }
42 my %saw;
43 @saw{@sizes}=();
44 my @keya= keys %saw;
45 #print scalar(@keya),"\n";
46 if(scalar(@keya)==1)
47 {
48 print output $keya[0],"\n";
49 }
50
51 }
52 #close(fusefile);
53 close(output);
54 close(input2);
55 close(input1);