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

List of all members.


Class Summary

Synopsis

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

Description

    Given a mulitple 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 GenomicAlignBlock table and the conserved scores in the 
    ConservationScore table
 

Definition at line 34 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 constrained_element_method_link_type ()
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 do_transactions ()
public void fetch_input ()
public free_aligned_sequence ()
public genomic_align_block_id ()
public get_params ()
public go_figure_dbc ()
public void info ()
public input_id ()
public
Bio::EnsEMBL::Hive::AnalysisJob 
input_job ()
public new ()
public no_conservation_scores ()
public options ()
public Array output ()
public param ()
public param_defaults ()
public param_file ()
public param_file_tmp ()
public param_substitute ()
public parameters ()
public program ()
public program_file ()
public program_version ()
public Bio::EnsEMBL::Hive::Queen queen ()
public void run ()
public run_gerp ()
public run_gerp_v2 ()
public Arrayref runnable ()
public species_set ()
public species_to_skip ()
public Array stack_trace ()
public String stack_trace_dump ()
public strict_hash_format ()
public void throw ()
public tree_analysis_data_id ()
public tree_file ()
public Depend try ()
public Int verbose ()
public warning ()
public window_sizes ()
public worker ()
public worker_temp_directory ()
public Boolean write_output ()

Method Documentation

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

Undocumented method

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protected Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Gerp::_calculateNeutralRate ( )

Undocumented method

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

Undocumented method

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

Undocumented method

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

Undocumented method

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

Undocumented method

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

Undocumented method

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

Undocumented method

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

Undocumented method

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

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Gerp::constrained_element_method_link_type ( )

Undocumented method

public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Gerp::do_transactions ( )

Undocumented method

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

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

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Gerp::genomic_align_block_id ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Gerp::get_params ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Gerp::no_conservation_scores ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Gerp::options ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Gerp::param_file ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Gerp::param_file_tmp ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Gerp::program ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Gerp::program_file ( )

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Gerp::program_version ( )

Undocumented method

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

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

Undocumented method

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

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Gerp::species_set ( )

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Gerp::species_to_skip ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Gerp::tree_analysis_data_id ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Gerp::tree_file ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Gerp::window_sizes ( )

Undocumented method

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


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