Mercurial > repos > portiahollyoak > temp
view scripts/pickUniqPos.pl @ 21:9672fe07a232 draft default tip
planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
author | mvdbeek |
---|---|
date | Mon, 05 Dec 2016 09:58:47 -0500 |
parents | e19d9742c99b |
children |
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#!/share/bin/perl use Bio::Seq; use List::Util qw(sum); die "perl $0 <sam>\n" if @ARGV<1; open in,$ARGV[0]; my %pe; while(<in>) { chomp; my @f=split/\t/,$_,12; ## read number 1 or 2 #my ($rnum)=$f[1]=~/(\d)$/; my $rnum=1; if (($f[1] & 128) == 128) {$rnum=2;} ## XT:A:* my ($xt)=$f[11]=~/XT:A:(.)/; my $strand="+"; ## revcomp if(($f[1] & 16) == 16) { my $seq=Bio::Seq->new(-seq=>$f[9], -alphabet => 'dna'); $f[9]=$seq->revcom->seq; $strand="-"; } ## parse CIGAR if($xt eq "U") { # CIGAR my (@cigar_m)=$f[5]=~/(\d+)M/g; my (@cigar_d)=$f[5]=~/(\d+)D/g; my (@cigar_s)=$f[5]=~/(\d+)S/g; my (@cigar_i)=$f[5]=~/(\d+)I/g; my $aln_ln=sum(@cigar_m,@cigar_d); print $f[2],"\t",$f[3]-1,"\t",$f[3]-1+$aln_ln,"\t$f[0]/$rnum\t",$f[9],"\t",$strand,"\n"; } } close in;