Mercurial > repos > portiahollyoak > temp
comparison scripts/pickUniqPos.pl.orig @ 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 | |
| children |
comparison
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| 20:6e02b9179a24 | 21:9672fe07a232 |
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| 1 #!/share/bin/perl | |
| 2 use Bio::Seq; | |
| 3 use List::Util qw(sum); | |
| 4 | |
| 5 die "perl $0 <sam>\n" if @ARGV<1; | |
| 6 open in,$ARGV[0]; | |
| 7 my %pe; | |
| 8 while(<in>) | |
| 9 { | |
| 10 chomp; | |
| 11 my @f=split/\t/,$_,12; | |
| 12 ## read number 1 or 2 | |
| 13 my ($rnum)=$f[1]=~/(\d)$/; | |
| 14 | |
| 15 ## XT:A:* | |
| 16 my ($xt)=$f[11]=~/XT:A:(.)/; | |
| 17 | |
| 18 my $strand="+"; | |
| 19 ## revcomp | |
| 20 if($f[1]=~/r/) | |
| 21 { | |
| 22 my $seq=Bio::Seq->new(-seq=>$f[9], -alphabet => 'dna'); | |
| 23 $f[9]=$seq->revcom->seq; | |
| 24 $strand="-"; | |
| 25 } | |
| 26 | |
| 27 ## parse CIGAR | |
| 28 if($xt eq "U") | |
| 29 { | |
| 30 # CIGAR | |
| 31 my (@cigar_m)=$f[5]=~/(\d+)M/g; | |
| 32 my (@cigar_d)=$f[5]=~/(\d+)D/g; | |
| 33 my (@cigar_s)=$f[5]=~/(\d+)S/g; | |
| 34 my (@cigar_i)=$f[5]=~/(\d+)I/g; | |
| 35 my $aln_ln=sum(@cigar_m,@cigar_d); | |
| 36 | |
| 37 print $f[2],"\t",$f[3]-1,"\t",$f[3]-1+$aln_ln,"\t$f[0]/$rnum\t",$f[9],"\t",$strand,"\n"; | |
| 38 } | |
| 39 } | |
| 40 close in; | |
| 41 |