view variant_effect_predictor/Bio/EnsEMBL/Utils/Slice.pm @ 0:1f6dce3d34e0

Uploaded

=head1 LICENSE

  Copyright (c) 1999-2012 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

    http://www.ensembl.org/info/about/code_licence.html

=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <[e-mail]>.

  Questions may also be sent to the Ensembl help desk at
  <[e-mail]>.

=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 => $slice->seq_region_length,
         -COORD_SYSTEM      => $slice->coord_system,
         -ADAPTOR           => $slice->adaptor);
      $start += $multiple + 1;
    }
  }

  return \@out;
}



1;