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

List of all members.


Class Summary

Synopsis

This runnable can be used both as a Hive pipeline component or run in standalone mode.
At the moment Compara runs it standalone, EnsEMBL Genomes runs it in both modes.

In standalone mode you will need to set --reg_conf to your registry configuration file in order to access the core databases.
You will have to refer to your compara database either via the full URL or (if you have a corresponding registry entry) via registry.
Here are both examples:

    standaloneJob.pl Bio::EnsEMBL::Compara::RunnableDB::MemberDisplayLabelUpdater --reg_conf $ENSEMBL_CVS_ROOT_DIR/ensembl-compara/scripts/pipeline/production_reg_conf.pl --compara_db compara_homology_merged --debug 1

    standaloneJob.pl Bio::EnsEMBL::Compara::RunnableDB::MemberDisplayLabelUpdater --reg_conf $ENSEMBL_CVS_ROOT_DIR/ensembl-compara/scripts/pipeline/production_reg_conf.pl --compara_db mysql://ensadmin:${ENSADMIN_PSW}@compara3:3306/lg4_compara_homology_merged_64 --debug 1

You should be able to limit the set of species being updated by adding --species "[ 90, 3 ]" or --species "[ 'human', 'rat' ]"

Description

The module loops through all genome_dbs given via the parameter species and attempts to update any gene/translation with the display identifier from the core database.
If the list of genome_dbs is not specified, it will attempt all genome_dbs with entries in the member table.
This code uses direct SQL statements because of the relationship between translations and their display labels
being stored at the transcript level. If the DB changes this will break.
 

Definition at line 36 of file MemberDisplayLabelUpdater.pm.

Available Methods

protected _get_display_label_lookup ()
protected _get_members_by_source ()
protected _need_to_process_genome_db_source ()
protected _process ()
protected _process_genome_db ()
protected _update_display_labels ()
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 void fetch_input ()
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
Bio::EnsEMBL::Compara::RunnableDB::MemberDisplayIdUpdater 
new_without_hive ()
public Array output ()
public param ()
public param_defaults ()
public param_substitute ()
public parameters ()
public Bio::EnsEMBL::Hive::Queen queen ()
public void run ()
public run_without_hive ()
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 void write_output ()

Method Documentation

protected Bio::EnsEMBL::Compara::RunnableDB::MemberDisplayLabelUpdater::_get_display_label_lookup ( )

Undocumented method

Code:
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protected Bio::EnsEMBL::Compara::RunnableDB::MemberDisplayLabelUpdater::_get_members_by_source ( )

Undocumented method

Code:
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protected Bio::EnsEMBL::Compara::RunnableDB::MemberDisplayLabelUpdater::_need_to_process_genome_db_source ( )

Undocumented method

Code:
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protected Bio::EnsEMBL::Compara::RunnableDB::MemberDisplayLabelUpdater::_process ( )

Undocumented method

Code:
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protected Bio::EnsEMBL::Compara::RunnableDB::MemberDisplayLabelUpdater::_process_genome_db ( )

Undocumented method

Code:
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protected Bio::EnsEMBL::Compara::RunnableDB::MemberDisplayLabelUpdater::_update_display_labels ( )

Undocumented method

Code:
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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
 
Code:
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public void Bio::EnsEMBL::Compara::RunnableDB::MemberDisplayLabelUpdater::fetch_input ( )
    Title   :   fetch_input
    Usage   :   $self->fetch_input
    Function:   prepares global variables and DB connections
    Returns :   none
    Args    :   none
 
Code:
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Reimplemented from Bio::EnsEMBL::Hive::Process.

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::MemberDisplayIdUpdater Bio::EnsEMBL::Compara::RunnableDB::MemberDisplayLabelUpdater::new_without_hive ( )
  Arg [DB_ADAPTOR]              : (DBAdaptor) Compara DBAdaptor to use
  Arg [REPLACE]                 : (Boolean)   Forces the code to replace display labels 
  Arg [DIE_IF_NO_CORE_ADAPTOR]  : (Boolean)   Kills the process if there is no core adaptor
  Arg [GENOME_DB_IDS]           : (ArrayRef)  GenomeDB IDs to run this process over
  Arg [DEBUG]                   : (Boolean)   Force debug output to STDOUT
  Example    : See synopsis
  Description: Non-hive version of the object construction to be used with scripts
  Returntype : Bio::EnsEMBL::Compara::RunnableDB::MemberDisplayIdUpdater
  Exceptions : if DB_ADAPTOR was not given and was not a valid object
  Caller     : general
 
Code:
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public void Bio::EnsEMBL::Compara::RunnableDB::MemberDisplayLabelUpdater::run ( )
    Title   :   run
    Usage   :   $self->run
    Function:   Retrives the Members to update
    Returns :   none
    Args    :   none
 
Code:
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Reimplemented from Bio::EnsEMBL::Hive::Process.

public Bio::EnsEMBL::Compara::RunnableDB::MemberDisplayLabelUpdater::run_without_hive ( )
Performs fetch_input(), run() and write_output() calls in one method.
 
Code:
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public void Bio::EnsEMBL::Compara::RunnableDB::MemberDisplayLabelUpdater::write_output ( )
    Title   :   write_output
    Usage   :   $self->write_output
    Function:   Writes the display labels/members back to the Compara DB
    Returns :   none
    Args    :   none
 
Code:
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Reimplemented from Bio::EnsEMBL::Hive::Process.


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