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Bio::EnsEMBL::Compara::RunnableDB::Ortheus Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::RunnableDB::Ortheus:

List of all members.


Class Summary

Synopsis

Description

This module acts as a layer between the Hive system and the Bio::EnsEMBL::Analysis::Runnable::Ortheus
module since the ensembl-analysis API does not know about ensembl-compara
Ortheus wants the files to be provided in the same order as in the tree string. This module starts
by getting all the DnaFragRegions of the SyntenyRegion and then use them to edit the tree (some
nodes must be removed and other ones must be duplicated in order to cope with deletions and
duplications). The build_tree_string methods numbers the sequences in order and changes the
order of the dnafrag_regions array accordingly. Last, the dumpFasta() method dumps the sequences
according to the tree_string order.
This module can be used to include low coverage 2X genomes in the alignment. To do this, the pairwise BLASTZ_NET alignments between each 2X genome and a reference species (eg human) are retrieved from specified databases.
Ortheus also generates a set of aligned ancestral sequences. This module stores them in a core-like database.
 

Definition at line 40 of file Ortheus.pm.

Available Methods

protected _add_to_cluster ()
protected _add_to_different_cluster ()
protected _add_to_same_cluster ()
protected _build_2x_composite_seq ()
protected _build_tree_string ()
protected _cluster_regions ()
protected _create_block_frag_array ()
protected _create_span_frag_array ()
protected _dump_2x_fasta ()
protected Boolean _dump_fasta ()
protected _extract_sequence ()
protected _find_longest_region_in_cluster ()
protected _in_cluster ()
protected _load_2XGenomes ()
protected Listref _load_DnaFragRegions ()
protected _merge_clusters ()
protected _print_cluster ()
protected _trim_gab_left ()
protected _trim_gab_right ()
protected
Bio::EnsEMBL::Compara::NestedSet 
_update_tree ()
protected _write_gerp_dataflow ()
protected _write_output ()
public Bio::EnsEMBL::Analysis analysis ()
public catch ()
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 void deprecate ()
public DESTROY ()
public dnafrag_regions ()
public fasta_files ()
public void fetch_input ()
public get_species_tree ()
public go_figure_compara_dba ()
public go_figure_dbc ()
public void info ()
public input_dir ()
public input_id ()
public
Bio::EnsEMBL::Hive::AnalysisJob 
input_job ()
public new ()
public options ()
public Array output ()
public param ()
public param_defaults ()
public param_substitute ()
public parameters ()
public parse_results ()
public Bio::EnsEMBL::Hive::Queen queen ()
public remove_empty_cols ()
public run ()
public Arrayref runnable ()
public species_order ()
public Array stack_trace ()
public String stack_trace_dump ()
public strict_hash_format ()
public synteny_region_id ()
public void throw ()
public tree_string ()
public Depend try ()
public Int verbose ()
public warning ()
public worker ()
public worker_temp_directory ()
public write_output ()

Method Documentation

protected Bio::EnsEMBL::Compara::RunnableDB::Ortheus::_add_to_cluster ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::Ortheus::_add_to_different_cluster ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::Ortheus::_add_to_same_cluster ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::Ortheus::_build_2x_composite_seq ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::Ortheus::_build_tree_string ( )
  Arg [1]    : -none-
  Example    : $self->_build_tree_string();
  Description: This method sets the tree_string using the orginal
               species tree and the set of DnaFragRegions. The
               tree is edited by the _update_tree method which
               resort the DnaFragRegions (see _update_tree elsewwhere
               in this document)
  Returntype : -none-
  Exception  :
  Warning    :
 
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protected Bio::EnsEMBL::Compara::RunnableDB::Ortheus::_cluster_regions ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::Ortheus::_create_block_frag_array ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::Ortheus::_create_span_frag_array ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::Ortheus::_dump_2x_fasta ( )

Undocumented method

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protected Boolean Bio::EnsEMBL::Compara::RunnableDB::Ortheus::_dump_fasta ( )
  Arg [1]    : -none-
  Example    : $self->_dump_fasta();
  Description: Dumps FASTA files in the order given by the tree
               string (needed by Pecan). Resulting file names are
               stored using the fasta_files getter/setter
  Returntype : 1
  Exception  :
  Warning    :
 
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protected Bio::EnsEMBL::Compara::RunnableDB::Ortheus::_extract_sequence ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::Ortheus::_find_longest_region_in_cluster ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::Ortheus::_in_cluster ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::Ortheus::_load_2XGenomes ( )
  Arg [1]    : int syteny_region_id
  Arg [2]    : int analysis_data_id
  Description: Creates a fake assembly for each 2X genome by stitching
               together the BLASTZ_NET alignments found on this synteny_region
               between the reference species and each 2X genome. The list of
               the pairwise database locations and  
               Bio::EnsEMBL::Compara::MethodLinkSpeciesSet ids are obtained
               from the analysis_data_id. Creates a listref of genomic_align 
               fragments
  Returntype : 
  Exception  : 
  Warning    :
 
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protected Listref Bio::EnsEMBL::Compara::RunnableDB::Ortheus::_load_DnaFragRegions ( )
  Arg [1]    : int syteny_region_id
  Example    : $self->_load_DnaFragRegions();
  Description: Gets the list of DnaFragRegions for this
               syteny_region_id. Resulting DnaFragRegions are
               stored using the dnafrag_regions getter/setter.
  Returntype : listref of Bio::EnsEMBL::Compara::DnaFragRegion objects
  Exception  :
  Warning    :
 
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protected Bio::EnsEMBL::Compara::RunnableDB::Ortheus::_merge_clusters ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::Ortheus::_print_cluster ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::Ortheus::_trim_gab_left ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::Ortheus::_trim_gab_right ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::NestedSet Bio::EnsEMBL::Compara::RunnableDB::Ortheus::_update_tree ( )
  Arg [1]    : Bio::EnsEMBL::Compara::NestedSet $tree_root
  Example    : $self->_update_nodes_names($tree);
  Description: This method updates the tree by removing or
               duplicating the leaves according to the orginal
               tree and the set of DnaFragRegions. The tree nodes
               will be renamed seq1, seq2, seq3 and so on and the
               DnaFragRegions will be resorted in order to match
               the names of the nodes (the first DnaFragRegion will
               correspond to seq1, the second to seq2 and so on).
  Returntype : Bio::EnsEMBL::Compara::NestedSet (a tree)
  Exception  :
  Warning    :
 
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protected Bio::EnsEMBL::Compara::RunnableDB::Ortheus::_write_gerp_dataflow ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::Ortheus::_write_output ( )

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::Ortheus::dnafrag_regions ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::Ortheus::fasta_files ( )

Undocumented method

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

public Bio::EnsEMBL::Compara::RunnableDB::Ortheus::get_species_tree ( )

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::Ortheus::input_dir ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::Ortheus::options ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::Ortheus::parse_results ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::Ortheus::remove_empty_cols ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::Ortheus::run ( )

Undocumented method

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

public Bio::EnsEMBL::Compara::RunnableDB::Ortheus::species_order ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::Ortheus::synteny_region_id ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::Ortheus::tree_string ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::Ortheus::write_output ( )

Undocumented method

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


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