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Bio::EnsEMBL::Compara::Production::EPOanchors::GetBlastzOverlaps Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::Production::EPOanchors::GetBlastzOverlaps:

List of all members.


Class Summary

Synopsis

$exonate_anchors-\>fetch_input();
$exonate_anchors-\>run();
$exonate_anchors-\>write_output(); writes to database

Description

Given a database with anchor sequences and a target genome. This modules exonerates 
the anchors against the target genome. The required information (anchor batch size,
target genome file, exonerate parameters are provided by the analysis, analysis_job 
and analysis_data tables
This modules is part of the Ensembl project http://www.ensembl.org
Email compara@ebi.ac.uk
 

Definition at line 33 of file GetBlastzOverlaps.pm.

Available Methods

public Bio::EnsEMBL::Analysis analysis ()
public analysis_data ()
public analysis_data_id ()
public analysis_id ()
public catch ()
public void check_if_exit_cleanly ()
public configure_defaults ()
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_chunks ()
public dnafrag_overlaps ()
public fetch_input ()
public genome_db_ids ()
public genomic_align_block_adaptor ()
public genomic_aligns_on_ref_slice ()
public get_input_id ()
public get_parameters ()
public go_figure_dbc ()
public void info ()
public input_id ()
public
Bio::EnsEMBL::Hive::AnalysisJob 
input_job ()
public method_link_species_set_id ()
public method_type ()
public mlssids ()
public new ()
public Array output ()
public param ()
public param_defaults ()
public param_substitute ()
public parameters ()
public Bio::EnsEMBL::Hive::Queen queen ()
public ref_dnafrag ()
public ref_dnafrag_coords ()
public ref_dnafrag_id ()
public ref_dnafrag_strand ()
public reference_genome_db ()
public run ()
public Arrayref runnable ()
public Array stack_trace ()
public String stack_trace_dump ()
public strict_hash_format ()
public void throw ()
public tree_analysis_data_id ()
public Depend try ()
public Int verbose ()
public warning ()
public worker ()
public worker_temp_directory ()
public write_output ()

Method Documentation

public Bio::EnsEMBL::Compara::Production::EPOanchors::GetBlastzOverlaps::analysis_data ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::EPOanchors::GetBlastzOverlaps::analysis_data_id ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::EPOanchors::GetBlastzOverlaps::analysis_id ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::EPOanchors::GetBlastzOverlaps::configure_defaults ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::EPOanchors::GetBlastzOverlaps::dnafrag_chunks ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::EPOanchors::GetBlastzOverlaps::dnafrag_overlaps ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::EPOanchors::GetBlastzOverlaps::fetch_input ( )

Undocumented method

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

public Bio::EnsEMBL::Compara::Production::EPOanchors::GetBlastzOverlaps::genome_db_ids ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::EPOanchors::GetBlastzOverlaps::genomic_align_block_adaptor ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::EPOanchors::GetBlastzOverlaps::genomic_aligns_on_ref_slice ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::EPOanchors::GetBlastzOverlaps::get_input_id ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::EPOanchors::GetBlastzOverlaps::get_parameters ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::EPOanchors::GetBlastzOverlaps::method_link_species_set_id ( )

Undocumented method

public Bio::EnsEMBL::Compara::Production::EPOanchors::GetBlastzOverlaps::method_type ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::EPOanchors::GetBlastzOverlaps::mlssids ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::EPOanchors::GetBlastzOverlaps::ref_dnafrag ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::EPOanchors::GetBlastzOverlaps::ref_dnafrag_coords ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::EPOanchors::GetBlastzOverlaps::ref_dnafrag_id ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::EPOanchors::GetBlastzOverlaps::ref_dnafrag_strand ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::EPOanchors::GetBlastzOverlaps::reference_genome_db ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::EPOanchors::GetBlastzOverlaps::run ( )

Undocumented method

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

public Bio::EnsEMBL::Compara::Production::EPOanchors::GetBlastzOverlaps::tree_analysis_data_id ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::EPOanchors::GetBlastzOverlaps::write_output ( )

Undocumented method

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


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