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Bio::EnsEMBL::Compara::RunnableDB::Families::LoadUniProtIndex Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::RunnableDB::Families::LoadUniProtIndex:

List of all members.


Class Summary

Description

This RunnableDB uses 'mfetch' to get the list of Uniprot accession numbers and dataflows to actual loading jobs.
The format of the input_id follows the format of a Perl hash reference.
Examples:
  "{'uniprot_source' =\> 'SWISSPROT', taxon_id=\>4932}"      # loads all SwissProt for S.cerevisiae
  "{'uniprot_source' =\> 'SPTREMBL'}"                       # loads all SPTrEMBL Fungi/Metazoa
  "{'uniprot_source' =\> 'SPTREMBL', taxon_id=\>4932}"       # loads all SPTrEMBL for S.cerevisiae
  "{'uniprot_source' =\> 'SWISSPROT', 'tax_div' =\> 'FUN'}"  # loads all SwissProt fungi proteins
  "{'uniprot_source' =\> 'SPTREMBL',  'tax_div' =\> 'ROD'}"  # loads all SwissProt rodent proteins
supported keys:
  uniprot_source    =>  'SWISSPROT' or 'SPTREMBL'
  taxon_id          => <taxon_id>
                            optional if one wants to load from a specific species
                            if not specified it will load all Fungi/Metazoa from the uniprot_source 
  tax_div           => <tax_div>
                            optional taxonomic division
 

Definition at line 28 of file LoadUniProtIndex.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 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 mfetch_uniprot_ids ()
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::Families::LoadUniProtIndex::fetch_input ( )

Undocumented method

Code:
click to view

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::Families::LoadUniProtIndex::mfetch_uniprot_ids ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::RunnableDB::Families::LoadUniProtIndex::param_defaults ( )

Undocumented method

Code:
click to view

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

public Bio::EnsEMBL::Compara::RunnableDB::Families::LoadUniProtIndex::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: