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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 =head1 NAME
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20
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21 Bio::EnsEMBL::Compara::GeneTreeNode
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22
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23 =head1 DESCRIPTION
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24
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25 Specific subclass of NestedSet to add functionality when the nodes of this tree
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26 are GeneTreeMember objects and the tree is a representation of a gene derived
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27 Phylogenetic tree
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28
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29 =head1 INHERITANCE TREE
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30
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31 Bio::EnsEMBL::Compara::GeneTreeNode
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32 `- Bio::EnsEMBL::Compara::NestedSet
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33
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34 =head1 AUTHORSHIP
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35
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36 Ensembl Team. Individual contributions can be found in the CVS log.
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37
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38 =head1 MAINTAINER
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39
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40 $Author: mm14 $
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41
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42 =head VERSION
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43
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44 $Revision: 1.15 $
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45
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46 =head1 APPENDIX
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47
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48 The rest of the documentation details each of the object methods.
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49 Internal methods are usually preceded with an underscore (_)
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50
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51 =cut
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52
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53 package Bio::EnsEMBL::Compara::GeneTreeNode;
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54
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55 use strict;
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56
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57 use IO::File;
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58
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59 use Bio::EnsEMBL::Utils::Argument;
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60 use Bio::EnsEMBL::Utils::Exception;
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61
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62 use Bio::EnsEMBL::Compara::AlignedMemberSet;
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63
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64 use base ('Bio::EnsEMBL::Compara::NestedSet');
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65
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66
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67 sub tree {
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68 my $self = shift;
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69 if (@_) {
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70 $self->{'_tree'} = shift;
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71 } elsif ((not defined $self->{'_tree'}) and (defined $self->adaptor) and (defined $self->{_root_id})) {
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72 $self->{'_tree'} = $self->adaptor->db->get_GeneTreeAdaptor->fetch_by_root_id($self->{_root_id});
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73 }
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74 return $self->{'_tree'};
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75 }
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76
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77
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78 # tweaked to take into account the GeneTree object
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79 sub root {
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80 my $self = shift;
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81 if (defined $self->tree) {
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82 return $self->tree->root;
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83 } else {
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84 return $self->SUPER::root;
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85 }
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86 }
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87
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88
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89 =head2 release_tree
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90
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91 Overview : Removes the to/from GeneTree reference to
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92 allow freeing memory
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93 Example : $self->release_tree;
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94 Returntype : undef
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95 Exceptions : none
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96 Caller : general
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97
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98 =cut
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99
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100 sub release_tree {
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101 my $self = shift;
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102
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103 if (defined $self->tree) {
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104 delete $self->{'_tree'}->{'_root'};
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105 delete $self->{'_tree'};
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106 }
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107 return $self->SUPER::release_tree;
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108 }
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109
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110
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111 #use Data::Dumper;
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112
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113 #sub string_node {
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114 # my $self = shift;
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115 # my $str = $self->SUPER::string_node;
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116 # if (defined $self->{'_tree'}) {
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117 # my $t = $self->{'_tree'};
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118 # $str = chop($str)." $t/root_id=".($self->{'_tree'}->root_id)."/".join("/", map { "$_ => ${$t}{$_}" } keys %$t)."\n";
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119 # }
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120 # return $str;
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121 #}
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122
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123 sub get_leaf_by_Member {
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124 my $self = shift;
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125 my $member = shift;
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126
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127 if($member->isa('Bio::EnsEMBL::Compara::GeneTreeNode')) {
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128 return $self->find_leaf_by_node_id($member->node_id);
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129 } elsif ($member->isa('Bio::EnsEMBL::Compara::Member')) {
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130 return $self->find_leaf_by_name($member->get_canonical_Member->stable_id);
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131 } else {
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132 die "Need a Member object!";
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133 }
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134 }
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135
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136 sub get_AlignedMemberSet {
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137 my $self = shift;
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138 my $set = Bio::EnsEMBL::Compara::AlignedMemberSet->new(
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139 -adaptor => $self->adaptor,
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140 -method_link_species_set_id => $self->tree->method_link_species_set_id,
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141 -stable_id => $self->tree->stable_id,
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142 -version => sprintf("%d.%d", $self->tree->version, $self->node_id),
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143 );
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144 foreach my $member (@{$self->get_all_leaves}) {
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145 $set->add_Member($member) if $member->isa('Bio::EnsEMBL::Compara::GeneTreeMember');
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146 }
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147 return $set;
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148 }
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149
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150 sub get_SimpleAlign {
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151 my $self = shift;
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152 return $self->get_AlignedMemberSet->get_SimpleAlign(@_);
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153 }
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154
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155 # Takes a protein tree and creates a consensus cigar line from the
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156 # constituent leaf nodes.
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157 sub consensus_cigar_line {
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158 my $self = shift;
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159 return $self->get_AlignedMemberSet->consensus_cigar_line(@_);
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160 }
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161
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162
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163
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164 =head2 remove_nodes_by_taxon_ids
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165
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166 Arg [1] : arrayref of taxon_ids
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167 Example : my $ret_tree = $tree->remove_nodes_by_taxon_ids($taxon_ids);
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168 Description : Returns the tree with removed nodes in taxon_id list.
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169 Returntype : Bio::EnsEMBL::Compara::GeneTreeNode object
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170 Exceptions :
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171 Caller : general
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172 Status : At risk (behaviour on exceptions could change)
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173
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174 =cut
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175
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176 sub remove_nodes_by_taxon_ids {
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177 my $self = shift;
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178 my $species_arrayref = shift;
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179
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180 my @tax_ids = @{$species_arrayref};
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181 # Turn the arrayref into a hash.
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182 my %tax_hash;
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183 map {$tax_hash{$_}=1} @tax_ids;
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184
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185 my @to_delete;
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186 foreach my $leaf (@{$self->get_all_leaves}) {
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187 if (exists $tax_hash{$leaf->taxon_id}) {
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188 push @to_delete, $leaf;
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189 }
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190 }
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191 return $self->remove_nodes(\@to_delete);
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192
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193 }
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194
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195
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196 =head2 keep_nodes_by_taxon_ids
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197
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198 Arg [1] : arrayref of taxon_ids
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199 Example : my $ret_tree = $tree->keep_nodes_by_taxon_ids($taxon_ids);
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200 Description : Returns the tree with kept nodes in taxon_id list.
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201 Returntype : Bio::EnsEMBL::Compara::GeneTreeNode object
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202 Exceptions :
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203 Caller : general
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204 Status : At risk (behaviour on exceptions could change)
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205
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206 =cut
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207
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208
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209 sub keep_nodes_by_taxon_ids {
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210 my $self = shift;
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211 my $species_arrayref = shift;
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212
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213 my @tax_ids = @{$species_arrayref};
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214 # Turn the arrayref into a hash.
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215 my %tax_hash;
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216 map {$tax_hash{$_}=1} @tax_ids;
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217
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218 my @to_delete;
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219 foreach my $leaf (@{$self->get_all_leaves}) {
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220 unless (exists $tax_hash{$leaf->taxon_id}) {
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221 push @to_delete, $leaf;
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222 }
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223 }
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224 return $self->remove_nodes(\@to_delete);
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225
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226 }
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227
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228 1;
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229
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