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

Uploaded

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+++ b/variant_effect_predictor/Bio/EnsEMBL/Compara/GeneTreeNode.pm	Fri Aug 03 10:04:48 2012 -0400
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+=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]>.
+
+=head1 NAME
+
+Bio::EnsEMBL::Compara::GeneTreeNode
+
+=head1 DESCRIPTION
+
+Specific subclass of NestedSet to add functionality when the nodes of this tree
+are GeneTreeMember objects and the tree is a representation of a gene derived
+Phylogenetic tree
+
+=head1 INHERITANCE TREE
+
+  Bio::EnsEMBL::Compara::GeneTreeNode
+  `- Bio::EnsEMBL::Compara::NestedSet
+
+=head1 AUTHORSHIP
+
+Ensembl Team. Individual contributions can be found in the CVS log.
+
+=head1 MAINTAINER
+
+$Author: mm14 $
+
+=head VERSION
+
+$Revision: 1.15 $
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods.
+Internal methods are usually preceded with an underscore (_)
+
+=cut
+
+package Bio::EnsEMBL::Compara::GeneTreeNode;
+
+use strict;
+
+use IO::File;
+
+use Bio::EnsEMBL::Utils::Argument;
+use Bio::EnsEMBL::Utils::Exception;
+
+use Bio::EnsEMBL::Compara::AlignedMemberSet;
+
+use base ('Bio::EnsEMBL::Compara::NestedSet');
+
+
+sub tree {
+    my $self = shift;
+    if (@_) {
+        $self->{'_tree'} = shift;
+    } elsif ((not defined $self->{'_tree'}) and (defined $self->adaptor) and (defined $self->{_root_id})) {
+        $self->{'_tree'} = $self->adaptor->db->get_GeneTreeAdaptor->fetch_by_root_id($self->{_root_id});
+    }
+    return $self->{'_tree'};
+}
+
+
+# tweaked to take into account the GeneTree object
+sub root {
+    my $self = shift;
+    if (defined $self->tree) {
+        return $self->tree->root;
+    } else {
+        return $self->SUPER::root;
+    }
+}
+
+
+=head2 release_tree
+
+  Overview   : Removes the to/from GeneTree reference to
+               allow freeing memory 
+  Example    : $self->release_tree;
+  Returntype : undef
+  Exceptions : none
+  Caller     : general
+
+=cut
+
+sub release_tree {
+    my $self = shift;
+
+    if (defined $self->tree) {
+        delete $self->{'_tree'}->{'_root'};
+        delete $self->{'_tree'};
+    }
+    return $self->SUPER::release_tree;
+}
+
+
+#use Data::Dumper;
+
+#sub string_node {
+#    my $self = shift;
+#    my $str = $self->SUPER::string_node;
+#    if (defined $self->{'_tree'}) {
+#        my $t = $self->{'_tree'};
+#        $str = chop($str)." $t/root_id=".($self->{'_tree'}->root_id)."/".join("/", map { "$_ => ${$t}{$_}" } keys %$t)."\n";
+#    }
+#    return $str;
+#}
+
+sub get_leaf_by_Member {
+  my $self = shift;
+  my $member = shift;
+
+  if($member->isa('Bio::EnsEMBL::Compara::GeneTreeNode')) {
+    return $self->find_leaf_by_node_id($member->node_id);
+  } elsif ($member->isa('Bio::EnsEMBL::Compara::Member')) {
+    return $self->find_leaf_by_name($member->get_canonical_Member->stable_id);
+  } else {
+    die "Need a Member object!";
+  }
+}
+
+sub get_AlignedMemberSet {
+    my $self = shift;
+    my $set = Bio::EnsEMBL::Compara::AlignedMemberSet->new(
+        -adaptor => $self->adaptor,
+        -method_link_species_set_id => $self->tree->method_link_species_set_id,
+        -stable_id => $self->tree->stable_id,
+        -version => sprintf("%d.%d", $self->tree->version, $self->node_id),
+    );
+    foreach my $member (@{$self->get_all_leaves}) {
+        $set->add_Member($member) if $member->isa('Bio::EnsEMBL::Compara::GeneTreeMember');
+    }
+    return $set;
+}
+
+sub get_SimpleAlign {
+    my $self = shift;
+    return $self->get_AlignedMemberSet->get_SimpleAlign(@_);
+}
+
+# Takes a protein tree and creates a consensus cigar line from the
+# constituent leaf nodes.
+sub consensus_cigar_line {
+    my $self = shift;
+    return $self->get_AlignedMemberSet->consensus_cigar_line(@_);
+}
+
+
+
+=head2 remove_nodes_by_taxon_ids
+
+  Arg [1]     : arrayref of taxon_ids
+  Example     : my $ret_tree = $tree->remove_nodes_by_taxon_ids($taxon_ids);
+  Description : Returns the tree with removed nodes in taxon_id list.
+  Returntype  : Bio::EnsEMBL::Compara::GeneTreeNode object
+  Exceptions  :
+  Caller      : general
+  Status      : At risk (behaviour on exceptions could change)
+
+=cut
+
+sub remove_nodes_by_taxon_ids {
+  my $self = shift;
+  my $species_arrayref = shift;
+
+  my @tax_ids = @{$species_arrayref};
+  # Turn the arrayref into a hash.
+  my %tax_hash;
+  map {$tax_hash{$_}=1} @tax_ids;
+
+  my @to_delete;
+  foreach my $leaf (@{$self->get_all_leaves}) {
+    if (exists $tax_hash{$leaf->taxon_id}) {
+      push @to_delete, $leaf;
+    }
+  }
+  return $self->remove_nodes(\@to_delete);
+
+}
+
+
+=head2 keep_nodes_by_taxon_ids
+
+  Arg [1]     : arrayref of taxon_ids
+  Example     : my $ret_tree = $tree->keep_nodes_by_taxon_ids($taxon_ids);
+  Description : Returns the tree with kept nodes in taxon_id list.
+  Returntype  : Bio::EnsEMBL::Compara::GeneTreeNode object
+  Exceptions  :
+  Caller      : general
+  Status      : At risk (behaviour on exceptions could change)
+
+=cut
+
+
+sub keep_nodes_by_taxon_ids {
+  my $self = shift;
+  my $species_arrayref = shift;
+
+  my @tax_ids = @{$species_arrayref};
+  # Turn the arrayref into a hash.
+  my %tax_hash;
+  map {$tax_hash{$_}=1} @tax_ids;
+
+  my @to_delete;
+  foreach my $leaf (@{$self->get_all_leaves}) {
+    unless (exists $tax_hash{$leaf->taxon_id}) {
+      push @to_delete, $leaf;
+    }
+  }
+  return $self->remove_nodes(\@to_delete);
+
+}
+
+1;
+