Mercurial > repos > portiahollyoak > temp
comparison scripts/pickUniqPos.pl @ 21:9672fe07a232 draft default tip
planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
author | mvdbeek |
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date | Mon, 05 Dec 2016 09:58:47 -0500 |
parents | e19d9742c99b |
children |
comparison
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20:6e02b9179a24 | 21:9672fe07a232 |
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8 while(<in>) | 8 while(<in>) |
9 { | 9 { |
10 chomp; | 10 chomp; |
11 my @f=split/\t/,$_,12; | 11 my @f=split/\t/,$_,12; |
12 ## read number 1 or 2 | 12 ## read number 1 or 2 |
13 my ($rnum)=$f[1]=~/(\d)$/; | 13 #my ($rnum)=$f[1]=~/(\d)$/; |
14 my $rnum=1; | |
15 if (($f[1] & 128) == 128) {$rnum=2;} | |
14 | 16 |
15 ## XT:A:* | 17 ## XT:A:* |
16 my ($xt)=$f[11]=~/XT:A:(.)/; | 18 my ($xt)=$f[11]=~/XT:A:(.)/; |
17 | 19 |
18 my $strand="+"; | 20 my $strand="+"; |
19 ## revcomp | 21 ## revcomp |
20 if($f[1]=~/r/) | 22 if(($f[1] & 16) == 16) |
21 { | 23 { |
22 my $seq=Bio::Seq->new(-seq=>$f[9], -alphabet => 'dna'); | 24 my $seq=Bio::Seq->new(-seq=>$f[9], -alphabet => 'dna'); |
23 $f[9]=$seq->revcom->seq; | 25 $f[9]=$seq->revcom->seq; |
24 $strand="-"; | 26 $strand="-"; |
25 } | 27 } |