Mercurial > repos > chawhwa > neuma
comparison NEUMA-1.2.1/bowtieout2insertlendis.PE.pl @ 0:c44c43d185ef draft default tip
NEUMA-1.2.1 Uploaded
| author | chawhwa |
|---|---|
| date | Thu, 08 Aug 2013 00:46:13 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:c44c43d185ef |
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| 1 #!/usr/bin/perl | |
| 2 | |
| 3 if(@ARGV<2) { print "usage: $0 bowtiefile readlength > insertlendis_file\n"; exit; } | |
| 4 | |
| 5 my $bowtiefile = shift @ARGV; | |
| 6 my $readlength = shift @ARGV; | |
| 7 | |
| 8 | |
| 9 open BOWTIE, $bowtiefile or die "Can't open bowtieout file $bowtiefile\n"; | |
| 10 while(<BOWTIE>){ | |
| 11 chomp; | |
| 12 my ($pos1) = (split/\t/)[3]; | |
| 13 chomp(my $secondline = <BOWTIE>); | |
| 14 my ($pos2) = (split/\t/,$secondline)[3]; | |
| 15 my $dist = $pos2 + $readlength - $pos1; | |
| 16 $Insert_lendis[$dist]++; | |
| 17 | |
| 18 } | |
| 19 close BOWTIE; | |
| 20 | |
| 21 | |
| 22 for my $i (0..$#Insert_lendis){ | |
| 23 print "$i\t$Insert_lendis[$i]\n" if defined($Insert_lendis[$i]); | |
| 24 } | |
| 25 |