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

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
 

Definition at line 29 of file ExonerateAnchors.pm.

Available Methods

public Bio::EnsEMBL::Analysis analysis ()
public analysis_data_id ()
public analysis_id ()
public anchor_sequences_mlssid ()
public ancs_from_to ()
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 exo_file ()
public exonerate_mlssid ()
public exonerate_options ()
public fetch_input ()
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 merge_overlapping_target_regions ()
public new ()
public Array output ()
public param ()
public param_defaults ()
public param_substitute ()
public parameters ()
public process_exonerate_hits ()
public Bio::EnsEMBL::Hive::Queen queen ()
public query_file ()
public run ()
public Arrayref runnable ()
public Array stack_trace ()
public String stack_trace_dump ()
public strict_hash_format ()
public target_file ()
public target_genome_db_id ()
public void throw ()
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::ExonerateAnchors::analysis_data_id ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::EPOanchors::ExonerateAnchors::analysis_id ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::EPOanchors::ExonerateAnchors::anchor_sequences_mlssid ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::EPOanchors::ExonerateAnchors::ancs_from_to ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::EPOanchors::ExonerateAnchors::configure_defaults ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::EPOanchors::ExonerateAnchors::exo_file ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::EPOanchors::ExonerateAnchors::exonerate_mlssid ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::EPOanchors::ExonerateAnchors::exonerate_options ( )

Undocumented method

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

Undocumented method

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

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

Undocumented method

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

Undocumented method

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public Bio::EnsEMBL::Compara::Production::EPOanchors::ExonerateAnchors::merge_overlapping_target_regions ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::EPOanchors::ExonerateAnchors::process_exonerate_hits ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::EPOanchors::ExonerateAnchors::query_file ( )

Undocumented method

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

Undocumented method

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

public Bio::EnsEMBL::Compara::Production::EPOanchors::ExonerateAnchors::target_file ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::EPOanchors::ExonerateAnchors::target_genome_db_id ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::EPOanchors::ExonerateAnchors::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: