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Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::DumpMercatorFiles Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::DumpMercatorFiles:

List of all members.


Class Summary

Synopsis

Description

    Create Chromosome, Anchor and Hit files needed by Mercator.
Supported keys:
    'genome_db_id' => <number>
        The id of the query genome
     'genome_db_ids' => < list_of_genome_db_ids >
        eg genome_db_ids => ' [61,108,111,112,38,60,101,43,31] '
        List of genome ids to match against
     'all_hits' => <0|1>
        Whether to perform all best hits (1) or best reciprocal hits only (0)
     'input_dir' => < directory_path >
        Location to write files required by Mercator
     'maximum_gap' => <number>
        eg 50000
     'cutoff_score' => <number>
         Filter by score. Not normally used
     'cutoff_evalue' => <number>
         Filter by evalue. Not normally used
 

Definition at line 44 of file DumpMercatorFiles.pm.

Available Methods

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 dumpMercatorFiles ()
public fetch_input ()
public get_sql_for_peptide_hits ()
public get_table_name_from_dbID ()
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 run ()
public Arrayref runnable ()
public Array stack_trace ()
public String stack_trace_dump ()
public strict_hash_format ()
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::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
 
Code:
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public Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::DumpMercatorFiles::dumpMercatorFiles ( )

Undocumented method

Code:
click to view
public Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::DumpMercatorFiles::fetch_input ( )

Undocumented method

Code:
click to view

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

public Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::DumpMercatorFiles::get_sql_for_peptide_hits ( )

Undocumented method

Code:
click to view
public Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::DumpMercatorFiles::get_table_name_from_dbID ( )

Undocumented method

Code:
click to view
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.
 
Code:
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public Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::DumpMercatorFiles::run ( )

Undocumented method

Code:
click to view

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

public Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::DumpMercatorFiles::write_output ( )

Undocumented method

Code:
click to view

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


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