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root/gclib/scripts/bowtie_rangeflt.pl
Revision: 24
Committed: Tue Jul 26 21:46:39 2011 UTC (8 years, 1 month ago) by gpertea
File size: 1069 byte(s)
Log Message:
Line File contents
1 #!/usr/bin/perl
2 use strict;
3 use Getopt::Std;
4 use FindBin;use lib $FindBin::Bin;
5
6 my $usage = q/Usage:
7 bowtie_rangeflt.pl <chr>[<strand>]:<start_coord>-<end_coord> bowtie_map_data..
8
9 Show only those bowtie mappings found in the specified genomic region.
10 /;
11 umask 0002;
12 getopts('o:') || die($usage."\n");
13 my $outfile=$Getopt::Std::opt_o;
14 die($usage."\n") unless $ARGV[0];
15 my $range=shift(@ARGV);
16 my ($chr, $start_coord, $end_coord)=
17 ($range=~m/^([^\:]+)\:(\d+)[\.\-]+(\d+)/);
18 die("$usage\n") unless $start_coord>=1 && $end_coord>$start_coord;
19 my $strand=$1 if ($chr=~s/([\-\+])$//);
20 if ($outfile) {
21 open(OUTF, '>'.$outfile) || die("Error creating output file $outfile\n");
22 select(OUTF);
23 }
24 while (<>) {
25 my $line=$_;
26 chomp;
27 my @t=split(/\t/);
28 my $mlen=length($t[4]);
29 next if $strand && $strand ne $t[1];
30 next if $chr && $chr ne $t[2];
31 next if ($start_coord && $t[3]+$mlen<$start_coord);
32 next if ($end_coord && $t[3]>=$end_coord);
33 print $line;
34 }
35 # --
36 if ($outfile) {
37 select(STDOUT);
38 close(OUTF);
39 }
40
41 #************ Subroutines **************

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