Raw content of Bio::EnsEMBL::Utils::Slice
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
Bio::EnsEMBL::Utils::Slice - Utility functions for slices
=head1 SYNOPSIS
use Bio::EnsEMBL::Utils::Slice qw(split_Slices);
# ...
# get all chromosomes in the database
my $slices = $slice_adaptor->fetch_all('chromosome');
# split the chromosomes into equal chunks of size less than 1MB
# with an overlap of 1kb
$slices = split_Slices( $slices, 1e6, 1e3 );
=head1 METHODS
=cut
package Bio::EnsEMBL::Utils::Slice;
use strict;
use warnings;
use Exporter;
use vars qw(@ISA @EXPORT_OK);
@ISA = qw(Exporter);
@EXPORT_OK = qw(&split_Slices);
use Bio::EnsEMBL::Utils::Exception qw(throw);
use POSIX;
=head2 split_Slices
Arg [1] : ref to list of slices
Arg [2] : int maxlength of sub slices
Arg [3] : int overlap length (optional)
Example : my $sub_slices = split_Slices($slices,$maxlen,$overlap)
Description: splits a slice into smaller slices
Returntype : ref to list of slices
Exceptions : maxlen <1 or overlap < 0
=cut
sub split_Slices{
my ($slice_big,$max_length,$overlap)=@_;
if(!defined($max_length) or $max_length < 1){
throw("maxlength needs to be set and > 0");
}
if(!defined($overlap)){
$overlap = 0;
}
elsif($overlap < 0){
throw("negative overlaps not allowed");
}
my @out=();
foreach my $slice (@$slice_big){
my $start = $slice->start;
my $end;
my $multiple;
my $number;
my $length = $slice->length;
if($max_length && ($length > $overlap)) {
#No seq region may be longer than max_length but we want to make
#them all similar size so that the last one isn't much shorter.
#Divide the seq_region into the largest equal pieces that are shorter
#than max_length
#calculate number of slices to create
$number = ($length-$overlap) / ($max_length-$overlap);
$number = ceil($number); #round up to int
#calculate length of created slices
$multiple = $length / $number;
$multiple = floor($multiple); #round down to int
} else {
#just one slice of the whole seq_region
$number = 1;
$multiple = $length;
}
my $i;
for(my $i=0; $i < $number; $i++) {
$end = $start + $multiple + $overlap;
#any remainder gets added to the last slice of the seq_region
$end = $slice->end if($i == $number-1);
push @out, Bio::EnsEMBL::Slice->new
(-START => $start,
-END => $end,
-STRAND => 1,
-SEQ_REGION_NAME => $slice->seq_region_name,
-SEQ_REGION_LENGTH => $length,
-COORD_SYSTEM => $slice->coord_system,
-ADAPTOR => $slice->adaptor);
$start += $multiple + 1;
}
}
return \@out;
}
1;
]]>