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1 =head1 LICENSE
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2
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3 Copyright (c) 1999-2012 The European Bioinformatics Institute and
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4 Genome Research Limited. All rights reserved.
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5
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6 This software is distributed under a modified Apache license.
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7 For license details, please see
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8
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9 http://www.ensembl.org/info/about/code_licence.html
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10
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11 =head1 CONTACT
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12
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13 Please email comments or questions to the public Ensembl
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14 developers list at <dev@ensembl.org>.
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15
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16 Questions may also be sent to the Ensembl help desk at
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17 <helpdesk@ensembl.org>.
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18
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19 =cut
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20
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21 =head1 NAME
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22
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23 Bio::EnsEMBL::Utils::Slice - Utility functions for slices
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24
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25 =head1 SYNOPSIS
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26
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27 use Bio::EnsEMBL::Utils::Slice qw(split_Slices);
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28
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29 # ...
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30
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31 # get all chromosomes in the database
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32 my $slices = $slice_adaptor->fetch_all('chromosome');
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33
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34 # split the chromosomes into equal chunks of size less than 1MB
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35 # with an overlap of 1kb
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36 $slices = split_Slices( $slices, 1e6, 1e3 );
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37
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38 =head1 METHODS
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39
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40 =cut
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41
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42
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43 package Bio::EnsEMBL::Utils::Slice;
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44
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45 use strict;
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46 use warnings;
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47
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48 use Exporter;
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49
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50 use vars qw(@ISA @EXPORT_OK);
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51
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52 @ISA = qw(Exporter);
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53
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54 @EXPORT_OK = qw(&split_Slices);
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55
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56 use Bio::EnsEMBL::Utils::Exception qw(throw);
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57 use POSIX;
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58
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59 =head2 split_Slices
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60
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61 Arg [1] : ref to list of slices
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62 Arg [2] : int maxlength of sub slices
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63 Arg [3] : int overlap length (optional)
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64 Example : my $sub_slices = split_Slices($slices,$maxlen,$overlap)
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65 Description: splits a slice into smaller slices
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66 Returntype : ref to list of slices
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67 Exceptions : maxlen <1 or overlap < 0
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68
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69 =cut
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70
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71 sub split_Slices{
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72 my ($slice_big,$max_length,$overlap)=@_;
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73
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74 if(!defined($max_length) or $max_length < 1){
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75 throw("maxlength needs to be set and > 0");
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76 }
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77
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78 if(!defined($overlap)){
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79 $overlap = 0;
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80 }
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81 elsif($overlap < 0){
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82 throw("negative overlaps not allowed");
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83 }
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84
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85 my @out=();
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86
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87 foreach my $slice (@$slice_big){
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88
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89 my $start = $slice->start;
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90 my $end;
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91 my $multiple;
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92 my $number;
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93 my $length = $slice->length;
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94
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95 if($max_length && ($length > $overlap)) {
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96 #No seq region may be longer than max_length but we want to make
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97 #them all similar size so that the last one isn't much shorter.
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98 #Divide the seq_region into the largest equal pieces that are shorter
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99 #than max_length
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100
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101 #calculate number of slices to create
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102 $number = ($length-$overlap) / ($max_length-$overlap);
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103 $number = ceil($number); #round up to int
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104
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105 #calculate length of created slices
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106 $multiple = $length / $number;
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107 $multiple = floor($multiple); #round down to int
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108 } else {
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109 #just one slice of the whole seq_region
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110 $number = 1;
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111 $multiple = $length;
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112 }
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113
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114 my $i;
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115 for(my $i=0; $i < $number; $i++) {
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116 $end = $start + $multiple + $overlap;
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117
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118 #any remainder gets added to the last slice of the seq_region
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119 $end = $slice->end if($i == $number-1);
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120 push @out, Bio::EnsEMBL::Slice->new
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121 (-START => $start,
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122 -END => $end,
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123 -STRAND => 1,
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124 -SEQ_REGION_NAME => $slice->seq_region_name,
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125 -SEQ_REGION_LENGTH => $slice->seq_region_length,
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126 -COORD_SYSTEM => $slice->coord_system,
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127 -ADAPTOR => $slice->adaptor);
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128 $start += $multiple + 1;
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129 }
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130 }
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131
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132 return \@out;
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133 }
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134
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135
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136
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137 1;
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