Mercurial > repos > yusuf > extend_bed_regions
diff extend_bed_regions @ 0:cb1c17dddc14 default tip
initial commit
author | Yusuf Ali <ali@yusuf.email> |
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date | Wed, 25 Mar 2015 13:32:42 -0600 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/extend_bed_regions Wed Mar 25 13:32:42 2015 -0600 @@ -0,0 +1,66 @@ +#!/usr/bin/env perl + +use strict; +use warnings; + +# This script adds up to X bases to either end of BED file regions (CAN BE NEGATIVE). The tool will merge regions that overlap after the expansion. +@ARGV == 4 or die "Usage: $0 <input regions.bed> <# bases> <5|3|both> <output.bed>\nWhere 5, 3 or both controls which flank is modified\n"; + +my $extension = $ARGV[1]; +my $ends = $ARGV[2]; + +my %chrs; +my @chr_names; +open(BED, $ARGV[0]) + or die "Cannot open $ARGV[0] for reading: $!\n"; +# assuming input in sorted by start per contig +while(<BED>){ + chomp; + my @F = split /\t/, $_; + my $strand = @F > 5 ? $F[5] : "+"; # is the strand field present? + my $start; + my $stop; + if($strand eq "+"){ + if($ends eq "both" or $ends eq "5"){ + $start = $F[1]-$extension; + $start = 1 if $start < 1; + } + if($ends eq "both" or $ends eq "3"){ + $stop = $F[2]+$extension; # can't check if okay unless we knew the chr sizes... + } + } + else{ + # negative strand + if($ends eq "both" or $ends eq "3"){ + $start = $F[1]-$extension; + $start = 1 if $start < 1; + } + if($ends eq "both" or $ends eq "5"){ + $stop = $F[2]+$extension; # can't check if okay unless we knew the chr sizes... + } + } + if(not exists $chrs{$F[0]}){ + $chrs{$F[0]} = [[$start,$stop]]; + push @chr_names, $F[0]; + next; + } + my $last_interval = $chrs{$F[0]}->[$#{$chrs{$F[0]}}]; + if($start <= $last_interval->[1]){ #overlaps previous + if($stop > $last_interval->[1]){ # extends beyond previous + $last_interval->[1] = $stop; + } #else it doesn't contribute new bases + } + else{ # standalone + push @{$chrs{$F[0]}}, [$start, $stop]; + } +} +close(BED); + +open(OUTPUT_BED, ">$ARGV[3]") + or die "Cannot open $ARGV[3] for writing: $!\n"; +for my $chr_name (@chr_names){ + for my $interval (@{$chrs{$chr_name}}){ + print OUTPUT_BED join("\t",$chr_name,$interval->[0],$interval->[1]), "\n"; + } +} +close(OUTPUT_BED);