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#!/usr/bin/perl |
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use strict; |
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use Getopt::Std; |
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use FindBin;use lib $FindBin::Bin; |
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|
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my $usage = q/Usage: |
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bowtie_rangeflt.pl <chr>[<strand>]:<start_coord>-<end_coord> bowtie_map_data.. |
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|
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Show only those bowtie mappings found in the specified genomic region. |
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/; |
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umask 0002; |
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getopts('o:') || die($usage."\n"); |
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my $outfile=$Getopt::Std::opt_o; |
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die($usage."\n") unless $ARGV[0]; |
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my $range=shift(@ARGV); |
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my ($chr, $start_coord, $end_coord)= |
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($range=~m/^([^\:]+)\:(\d+)[\.\-]+(\d+)/); |
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die("$usage\n") unless $start_coord>=1 && $end_coord>$start_coord; |
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my $strand=$1 if ($chr=~s/([\-\+])$//); |
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if ($outfile) { |
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open(OUTF, '>'.$outfile) || die("Error creating output file $outfile\n"); |
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select(OUTF); |
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} |
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while (<>) { |
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my $line=$_; |
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chomp; |
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my @t=split(/\t/); |
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my $mlen=length($t[4]); |
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next if $strand && $strand ne $t[1]; |
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next if $chr && $chr ne $t[2]; |
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next if ($start_coord && $t[3]+$mlen<$start_coord); |
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next if ($end_coord && $t[3]>=$end_coord); |
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print $line; |
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} |
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# -- |
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if ($outfile) { |
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select(STDOUT); |
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close(OUTF); |
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} |
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|
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#************ Subroutines ************** |
