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Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::LowCoverageGenomeAlignment Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::LowCoverageGenomeAlignment:

List of all members.


Class Summary

Synopsis

Description

This module acts as a layer between the Hive system and the Bio::EnsEMBL::Analysis::Runnable::LowCoverageGenomeAlignment module since the ensembl-analysis API does not know about ensembl-compara
This module is the alternative module to Ortheus.pm for aligning low coverage (2X) genomes. This takes an existing high coverage alignment and maps the pairwise BlastZ-Net alignments of the low coverage genomes to the human sequence in the high coverage alignment. Any insertions in the low coverage alignments are removed, that is, no gaps are added to the human sequence. In regions where there are duplications, a phylogenetic tree is generated using either treeBest where there are more than 3 sequences in the alignment or semphy where there are 3 or less sequences. This module is still under development.
 

Definition at line 25 of file LowCoverageGenomeAlignment.pm.

Available Methods

protected _add_to_cluster ()
protected _add_to_different_cluster ()
protected _add_to_same_cluster ()
protected _build_tree_string ()
protected _cluster_regions ()
protected _construct_pairwise_locations ()
protected _create_frag_array ()
protected _create_mfa ()
protected _dump_2x_fasta ()
protected Boolean _dump_fasta_and_mfa ()
protected _extract_sequence ()
protected _find_longest_region_in_cluster ()
protected _fix_internal_ids ()
protected _in_cluster ()
protected _load_2XGenomes ()
protected _load_GenomicAligns ()
protected _merge_clusters ()
protected void _parse_results ()
protected _print_cluster ()
protected
Bio::EnsEMBL::Compara::NestedSet 
_update_tree_2x ()
protected _write_gerp_dataflow ()
protected _write_output ()
public add_match_elem ()
public Bio::EnsEMBL::Analysis analysis ()
public catch ()
public check_cigar_line ()
public void check_if_exit_cleanly ()
public cigar_element ()
public compara_dba ()
public create_2x_cigar_line ()
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 fasta_files ()
public void fetch_input ()
public find_ref_deletions ()
public get_seq_length_from_cigar ()
public get_species_tree ()
public get_taxon_tree ()
public go_figure_compara_dba ()
public go_figure_dbc ()
public void info ()
public input_id ()
public
Bio::EnsEMBL::Hive::AnalysisJob 
input_job ()
public new ()
public Array output ()
public param ()
public param_defaults ()
public param_substitute ()
public parameters ()
public Bio::EnsEMBL::Hive::Queen queen ()
public void run ()
public Arrayref runnable ()
public species_order ()
public Array stack_trace ()
public String stack_trace_dump ()
public strict_hash_format ()
public void throw ()
public tree_string ()
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::EpoLowCoverage::LowCoverageGenomeAlignment::_add_to_cluster ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::LowCoverageGenomeAlignment::_add_to_different_cluster ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::LowCoverageGenomeAlignment::_add_to_same_cluster ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::LowCoverageGenomeAlignment::_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::EpoLowCoverage::LowCoverageGenomeAlignment::_cluster_regions ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::LowCoverageGenomeAlignment::_construct_pairwise_locations ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::LowCoverageGenomeAlignment::_create_frag_array ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::LowCoverageGenomeAlignment::_create_mfa ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::LowCoverageGenomeAlignment::_dump_2x_fasta ( )

Undocumented method

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protected Boolean Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::LowCoverageGenomeAlignment::_dump_fasta_and_mfa ( )
  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::EpoLowCoverage::LowCoverageGenomeAlignment::_extract_sequence ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::LowCoverageGenomeAlignment::_find_longest_region_in_cluster ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::LowCoverageGenomeAlignment::_fix_internal_ids ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::LowCoverageGenomeAlignment::_in_cluster ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::LowCoverageGenomeAlignment::_load_2XGenomes ( )
  Arg [1]    : int genomic_align_block_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 Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::LowCoverageGenomeAlignment::_load_GenomicAligns ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::LowCoverageGenomeAlignment::_merge_clusters ( )

Undocumented method

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protected void Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::LowCoverageGenomeAlignment::_parse_results ( )
    Arg        : none
    Example    : $self->_parse_results
    Description: parse the alignment and tree files
    Returntype : none
    Exceptions : 
    Caller     : run
    Status     : At risk
 
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protected Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::LowCoverageGenomeAlignment::_print_cluster ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::NestedSet Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::LowCoverageGenomeAlignment::_update_tree_2x ( )
  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::EpoLowCoverage::LowCoverageGenomeAlignment::_write_gerp_dataflow ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::LowCoverageGenomeAlignment::_write_output ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::LowCoverageGenomeAlignment::add_match_elem ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::LowCoverageGenomeAlignment::check_cigar_line ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::LowCoverageGenomeAlignment::cigar_element ( )

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::EpoLowCoverage::LowCoverageGenomeAlignment::create_2x_cigar_line ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::LowCoverageGenomeAlignment::fasta_files ( )

Undocumented method

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public void Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::LowCoverageGenomeAlignment::fetch_input ( )
    Arg        :   -none-
    Example    :   $self->fetch_input
    Description:   Fetches input data for the module from the database
    Returntype :   none
    Excptions  :
    Caller     :
    Status     :   At risk
 
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Reimplemented from Bio::EnsEMBL::Hive::Process.

public Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::LowCoverageGenomeAlignment::find_ref_deletions ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::LowCoverageGenomeAlignment::get_seq_length_from_cigar ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::LowCoverageGenomeAlignment::get_species_tree ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::LowCoverageGenomeAlignment::get_taxon_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 void Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::LowCoverageGenomeAlignment::run ( )
    Arg        : -none-
    Example    : $self->run
    Description: runs the  LowCoverageGenomeAlignment analysis module and 
                  parses the results
    Returntype : none
    Exceptions : none
    Caller     :
    Status     :   At risk
 
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Reimplemented from Bio::EnsEMBL::Hive::Process.

public Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::LowCoverageGenomeAlignment::species_order ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::LowCoverageGenomeAlignment::tree_string ( )

Undocumented method

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public void Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::LowCoverageGenomeAlignment::write_output ( )
    Arg        : -none
    Example    : $self->write_output
    Description: stores results in a database
    Returntype : none
    Exceptions : none
    Caller     :
    Status     : At risk
 
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Reimplemented from Bio::EnsEMBL::Hive::Process.


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