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Bio::EnsEMBL::Compara::RunnableDB::PairAligner::UcscToEnsemblMapping Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::RunnableDB::PairAligner::UcscToEnsemblMapping:

List of all members.


Class Summary

Synopsis

Description

Convert UCSC names to ensembl names (reference only chromosomes and supercontigs, ie no haplotypes)
First check the names using chromInfo.txt and then go to mapping file if necessary eg ctgPos.txt for human
Download from:
http://hgdownload.cse.ucsc.edu/downloads.html
Choose species
Choose Annotation database
wget http://hgdownload.cse.ucsc.edu/goldenPath/ponAbe2/database/chromInfo.txt.gz
 

Definition at line 25 of file UcscToEnsemblMapping.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 Nothing 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 Array output ()
public param ()
public param_defaults ()
public param_substitute ()
public parameters ()
public Bio::EnsEMBL::Hive::Queen queen ()
public read_ucsc_map ()
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:
click to view
public Nothing Bio::EnsEMBL::Compara::RunnableDB::PairAligner::UcscToEnsemblMapping::fetch_input ( )
    Title   :   fetch_input
    Usage   :   $self->fetch_input
    Returns :   nothing
    Args    :   none
 
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:
click to view
public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::UcscToEnsemblMapping::read_ucsc_map ( )

Undocumented method

Code:
click to view
public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::UcscToEnsemblMapping::run ( )

Undocumented method

Code:
click to view

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

public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::UcscToEnsemblMapping::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: