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Bio::EnsEMBL::Compara::RunnableDB::GenomicAlignBlock::Gerp Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::RunnableDB::GenomicAlignBlock::Gerp:

List of all members.


Class Summary

Synopsis

    $gerp-\>fetch_input();
    $gerp-\>run();
    $gerp-\>write_output(); writes to database

Description

    Given a multiple alignment Bio::EnsEMBL::Compara::DBSQL::GenomicAlignBlock 
    identifier it fetches GenomicAlignBlocks from a compara database and runs
    the program GERP.pl. It then parses the output and writes the constrained
    elements in the constrained_element table and the conserved scores in the 
    conservation_score table
 

Definition at line 33 of file Gerp.pm.

Available Methods

protected _build_tree_string ()
protected _calculateNeutralRate ()
protected _get_name_from_GenomicAlign ()
protected _parse_cons_file ()
protected _parse_rates_file ()
protected _parse_results ()
protected _parse_results_v2 ()
protected _update_tree ()
protected _write_output ()
protected _writeMultiFastaAlignment ()
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 free_aligned_sequence ()
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 void run ()
public run_gerp ()
public run_gerp_v2 ()
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 Boolean write_output ()

Method Documentation

protected Bio::EnsEMBL::Compara::RunnableDB::GenomicAlignBlock::Gerp::_build_tree_string ( )

Undocumented method

Code:
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protected Bio::EnsEMBL::Compara::RunnableDB::GenomicAlignBlock::Gerp::_calculateNeutralRate ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::GenomicAlignBlock::Gerp::_get_name_from_GenomicAlign ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::GenomicAlignBlock::Gerp::_parse_cons_file ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::GenomicAlignBlock::Gerp::_parse_rates_file ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::GenomicAlignBlock::Gerp::_parse_results ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::GenomicAlignBlock::Gerp::_parse_results_v2 ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::GenomicAlignBlock::Gerp::_update_tree ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::GenomicAlignBlock::Gerp::_write_output ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::RunnableDB::GenomicAlignBlock::Gerp::_writeMultiFastaAlignment ( )

Undocumented method

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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::GenomicAlignBlock::Gerp::fetch_input ( )
    Title   :   fetch_input
    Usage   :   $self->fetch_input
    Function:   Fetches input data for gerp from the database
    Returns :   none
    Args    :   none
 
Code:
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Reimplemented from Bio::EnsEMBL::Hive::Process.

public Bio::EnsEMBL::Compara::RunnableDB::GenomicAlignBlock::Gerp::free_aligned_sequence ( )

Undocumented method

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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.
 
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public Bio::EnsEMBL::Compara::RunnableDB::GenomicAlignBlock::Gerp::param_defaults ( )

Undocumented method

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

public void Bio::EnsEMBL::Compara::RunnableDB::GenomicAlignBlock::Gerp::run ( )
    Title   :   run
    Usage   :   $self->run
    Function:   Run gerp
    Returns :   none
    Args    :   none
 
Code:
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Reimplemented from Bio::EnsEMBL::Hive::Process.

public Bio::EnsEMBL::Compara::RunnableDB::GenomicAlignBlock::Gerp::run_gerp ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::GenomicAlignBlock::Gerp::run_gerp_v2 ( )

Undocumented method

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public Boolean Bio::EnsEMBL::Compara::RunnableDB::GenomicAlignBlock::Gerp::write_output ( )
    Title   :   write_output
    Usage   :   $self->write_output
    Function:   Write results to the database
    Returns :   1
    Args    :   none
 
Code:
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Reimplemented from Bio::EnsEMBL::Hive::Process.


The documentation for this class was generated from the following file:
  • Bio/EnsEMBL/Compara/RunnableDB/GenomicAlignBlock/Gerp.pm