comparison variant_effect_predictor/Bio/EnsEMBL/Compara/GeneTreeNode.pm @ 0:21066c0abaf5 draft

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author willmclaren
date Fri, 03 Aug 2012 10:04:48 -0400
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1 =head1 LICENSE
2
3 Copyright (c) 1999-2012 The European Bioinformatics Institute and
4 Genome Research Limited. All rights reserved.
5
6 This software is distributed under a modified Apache license.
7 For license details, please see
8
9 http://www.ensembl.org/info/about/code_licence.html
10
11 =head1 CONTACT
12
13 Please email comments or questions to the public Ensembl
14 developers list at <dev@ensembl.org>.
15
16 Questions may also be sent to the Ensembl help desk at
17 <helpdesk@ensembl.org>.
18
19 =head1 NAME
20
21 Bio::EnsEMBL::Compara::GeneTreeNode
22
23 =head1 DESCRIPTION
24
25 Specific subclass of NestedSet to add functionality when the nodes of this tree
26 are GeneTreeMember objects and the tree is a representation of a gene derived
27 Phylogenetic tree
28
29 =head1 INHERITANCE TREE
30
31 Bio::EnsEMBL::Compara::GeneTreeNode
32 `- Bio::EnsEMBL::Compara::NestedSet
33
34 =head1 AUTHORSHIP
35
36 Ensembl Team. Individual contributions can be found in the CVS log.
37
38 =head1 MAINTAINER
39
40 $Author: mm14 $
41
42 =head VERSION
43
44 $Revision: 1.15 $
45
46 =head1 APPENDIX
47
48 The rest of the documentation details each of the object methods.
49 Internal methods are usually preceded with an underscore (_)
50
51 =cut
52
53 package Bio::EnsEMBL::Compara::GeneTreeNode;
54
55 use strict;
56
57 use IO::File;
58
59 use Bio::EnsEMBL::Utils::Argument;
60 use Bio::EnsEMBL::Utils::Exception;
61
62 use Bio::EnsEMBL::Compara::AlignedMemberSet;
63
64 use base ('Bio::EnsEMBL::Compara::NestedSet');
65
66
67 sub tree {
68 my $self = shift;
69 if (@_) {
70 $self->{'_tree'} = shift;
71 } elsif ((not defined $self->{'_tree'}) and (defined $self->adaptor) and (defined $self->{_root_id})) {
72 $self->{'_tree'} = $self->adaptor->db->get_GeneTreeAdaptor->fetch_by_root_id($self->{_root_id});
73 }
74 return $self->{'_tree'};
75 }
76
77
78 # tweaked to take into account the GeneTree object
79 sub root {
80 my $self = shift;
81 if (defined $self->tree) {
82 return $self->tree->root;
83 } else {
84 return $self->SUPER::root;
85 }
86 }
87
88
89 =head2 release_tree
90
91 Overview : Removes the to/from GeneTree reference to
92 allow freeing memory
93 Example : $self->release_tree;
94 Returntype : undef
95 Exceptions : none
96 Caller : general
97
98 =cut
99
100 sub release_tree {
101 my $self = shift;
102
103 if (defined $self->tree) {
104 delete $self->{'_tree'}->{'_root'};
105 delete $self->{'_tree'};
106 }
107 return $self->SUPER::release_tree;
108 }
109
110
111 #use Data::Dumper;
112
113 #sub string_node {
114 # my $self = shift;
115 # my $str = $self->SUPER::string_node;
116 # if (defined $self->{'_tree'}) {
117 # my $t = $self->{'_tree'};
118 # $str = chop($str)." $t/root_id=".($self->{'_tree'}->root_id)."/".join("/", map { "$_ => ${$t}{$_}" } keys %$t)."\n";
119 # }
120 # return $str;
121 #}
122
123 sub get_leaf_by_Member {
124 my $self = shift;
125 my $member = shift;
126
127 if($member->isa('Bio::EnsEMBL::Compara::GeneTreeNode')) {
128 return $self->find_leaf_by_node_id($member->node_id);
129 } elsif ($member->isa('Bio::EnsEMBL::Compara::Member')) {
130 return $self->find_leaf_by_name($member->get_canonical_Member->stable_id);
131 } else {
132 die "Need a Member object!";
133 }
134 }
135
136 sub get_AlignedMemberSet {
137 my $self = shift;
138 my $set = Bio::EnsEMBL::Compara::AlignedMemberSet->new(
139 -adaptor => $self->adaptor,
140 -method_link_species_set_id => $self->tree->method_link_species_set_id,
141 -stable_id => $self->tree->stable_id,
142 -version => sprintf("%d.%d", $self->tree->version, $self->node_id),
143 );
144 foreach my $member (@{$self->get_all_leaves}) {
145 $set->add_Member($member) if $member->isa('Bio::EnsEMBL::Compara::GeneTreeMember');
146 }
147 return $set;
148 }
149
150 sub get_SimpleAlign {
151 my $self = shift;
152 return $self->get_AlignedMemberSet->get_SimpleAlign(@_);
153 }
154
155 # Takes a protein tree and creates a consensus cigar line from the
156 # constituent leaf nodes.
157 sub consensus_cigar_line {
158 my $self = shift;
159 return $self->get_AlignedMemberSet->consensus_cigar_line(@_);
160 }
161
162
163
164 =head2 remove_nodes_by_taxon_ids
165
166 Arg [1] : arrayref of taxon_ids
167 Example : my $ret_tree = $tree->remove_nodes_by_taxon_ids($taxon_ids);
168 Description : Returns the tree with removed nodes in taxon_id list.
169 Returntype : Bio::EnsEMBL::Compara::GeneTreeNode object
170 Exceptions :
171 Caller : general
172 Status : At risk (behaviour on exceptions could change)
173
174 =cut
175
176 sub remove_nodes_by_taxon_ids {
177 my $self = shift;
178 my $species_arrayref = shift;
179
180 my @tax_ids = @{$species_arrayref};
181 # Turn the arrayref into a hash.
182 my %tax_hash;
183 map {$tax_hash{$_}=1} @tax_ids;
184
185 my @to_delete;
186 foreach my $leaf (@{$self->get_all_leaves}) {
187 if (exists $tax_hash{$leaf->taxon_id}) {
188 push @to_delete, $leaf;
189 }
190 }
191 return $self->remove_nodes(\@to_delete);
192
193 }
194
195
196 =head2 keep_nodes_by_taxon_ids
197
198 Arg [1] : arrayref of taxon_ids
199 Example : my $ret_tree = $tree->keep_nodes_by_taxon_ids($taxon_ids);
200 Description : Returns the tree with kept nodes in taxon_id list.
201 Returntype : Bio::EnsEMBL::Compara::GeneTreeNode object
202 Exceptions :
203 Caller : general
204 Status : At risk (behaviour on exceptions could change)
205
206 =cut
207
208
209 sub keep_nodes_by_taxon_ids {
210 my $self = shift;
211 my $species_arrayref = shift;
212
213 my @tax_ids = @{$species_arrayref};
214 # Turn the arrayref into a hash.
215 my %tax_hash;
216 map {$tax_hash{$_}=1} @tax_ids;
217
218 my @to_delete;
219 foreach my $leaf (@{$self->get_all_leaves}) {
220 unless (exists $tax_hash{$leaf->taxon_id}) {
221 push @to_delete, $leaf;
222 }
223 }
224 return $self->remove_nodes(\@to_delete);
225
226 }
227
228 1;
229