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Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree:

List of all members.


Class Summary

Description

This Analysis/RunnableDB is designed to take ProteinTree as input
This must already have a rooted tree with duplication/sepeciation tags
on the nodes.
It analyzes that tree structure to pick Orthologues and Paralogs for
each genepair.
input_id/parameters format eg: "{'protein_tree_id'=\>1234}"
    protein_tree_id : use 'id' to fetch a cluster from the ProteinTree
 

Synopsis

my $db    = Bio::EnsEMBL::Compara::DBAdaptor-\>new($locator);
my $otree = Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree-\>new ( 
                                                    -db      =\> $db,
                                                    -input_id   =\> $input_id,
                                                    -analysis   =\> $analysis );
$otree-\>fetch_input(); #reads from DB
$otree-\>run();
$otree-\>output();
$otree-\>write_output(); #writes to DB

Definition at line 46 of file OrthoTree.pm.

Available Methods

protected _slurp ()
public Bio::EnsEMBL::Analysis analysis ()
public analyze_genepairlink ()
public ancient_residual_test ()
public catch ()
public check_homology_consistency ()
public void check_if_exit_cleanly ()
public compara_dba ()
public
Bio::EnsEMBL::DBSQL::DBConnection 
data_dbc ()
public dataflow_output_id ()
public
Bio::EnsEMBL::Hive::DBSQL::DBAdaptor 
db ()
public
Bio::EnsEMBL::DBSQL::DBConnection 
dbc ()
public Int debug ()
public delete_old_homologies ()
public delete_old_homologies_old ()
public delete_old_orthotree_tags ()
public void deprecate ()
public DESTROY ()
public direct_ortholog_test ()
public display_link_analysis ()
public duplication_confidence_score ()
public void fetch_input ()
public genepairlink_check_dups ()
public genepairlink_fetch_homology ()
public generate_attribute_arguments ()
public get_ancestor_species_hash ()
public get_ancestor_taxon_level ()
public get_matrix_hash ()
public get_species_tree_string ()
public go_figure_compara_dba ()
public go_figure_dbc ()
public void info ()
public input_id ()
public
Bio::EnsEMBL::Hive::AnalysisJob 
input_job ()
public inspecies_paralog_test ()
public load_species_tree_from_string ()
public new ()
public one2many_ortholog_test ()
public Array output ()
public outspecies_test ()
public param ()
public param_defaults ()
public param_substitute ()
public parameters ()
public Bio::EnsEMBL::Hive::Queen queen ()
public void run ()
public run_analysis ()
public Arrayref runnable ()
public Array stack_trace ()
public String stack_trace_dump ()
public store_gene_link_as_homology ()
public store_homologies ()
public strict_hash_format ()
public void throw ()
public Depend try ()
public Int verbose ()
public warning ()
public worker ()
public worker_temp_directory ()
public void write_output ()

Method Documentation

protected Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::_slurp ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::analyze_genepairlink ( )

Undocumented method

public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::ancient_residual_test ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::check_homology_consistency ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::BaseRunnable::compara_dba ( ) [inherited]
    Description: this is an intelligent setter/getter of a Compara DBA. Resorts to magic in order to figure out how to connect.
    Example 1:   my $family_adaptor = $self->compara_dba()->get_FamilyAdaptor();    # implicit initialization and hashing
    Example 2:   my $external_foo_adaptor = $self->compara_dba( $self->param('db_conn') )->get_FooAdaptor();    # explicit initialization and hashing
 
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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::delete_old_homologies ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::delete_old_homologies_old ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::delete_old_orthotree_tags ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::DESTROY ( )

Undocumented method

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Reimplemented from Bio::EnsEMBL::Hive::Process.

Reimplemented in Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::NJTREE_PHYML.

public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::direct_ortholog_test ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::display_link_analysis ( )

Undocumented method

public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::duplication_confidence_score ( )

Undocumented method

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public void Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::fetch_input ( )
    Title   :   fetch_input
    Usage   :   $self->fetch_input
    Function:   Fetches input data from the database
    Returns :   none
    Args    :   none
 
Code:
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Reimplemented from Bio::EnsEMBL::Hive::Process.

Reimplemented in Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::NJTREE_PHYML.

public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::genepairlink_check_dups ( )

Undocumented method

public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::genepairlink_fetch_homology ( )

Undocumented method

public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::generate_attribute_arguments ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::get_ancestor_species_hash ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::get_ancestor_taxon_level ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::get_matrix_hash ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::get_species_tree_string ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::BaseRunnable::go_figure_compara_dba ( ) [inherited]
    Description: this is a method that tries lots of different ways to find connection parameters
                 from a given object/hash and returns a Compara DBA. Does not hash anything, just does the detective magic.
 
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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::inspecies_paralog_test ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::load_species_tree_from_string ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::one2many_ortholog_test ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::outspecies_test ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::param_defaults ( )

Undocumented method

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Reimplemented from Bio::EnsEMBL::Hive::Process.

Reimplemented in Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::NJTREE_PHYML.

public void Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::run ( )
    Title   :   run
    Usage   :   $self->run
    Function:   runs OrthoTree
    Returns :   none
    Args    :   none
 
Code:
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Reimplemented from Bio::EnsEMBL::Hive::Process.

Reimplemented in Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::NJTREE_PHYML.

public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::run_analysis ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::store_gene_link_as_homology ( )

Undocumented method

public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::store_homologies ( )

Undocumented method

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public void Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree::write_output ( )
    Title   :   write_output
    Usage   :   $self->write_output
    Function: parse clustalw output and update homology and
              homology_member tables
    Returns : none 
    Args    : none
 
Code:
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Reimplemented from Bio::EnsEMBL::Hive::Process.

Reimplemented in Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::NJTREE_PHYML.


The documentation for this class was generated from the following file: