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

List of all members.


Class Summary

Synopsis

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

Description

    Given a genomic_align_tree Bio::EnsEMBL::Compara::DBSQL::GenomicAlignTree
    identifier it fetches the alignment and the tree from a compara database and runs
    the program phastCons. At the moment, only conserved elements are supported,
    the parser for conservation scores is not implemented yet.
    WARNING: This is preliminary version nd the paths/options/etc are hard-coded.
    Please, refer to the TODO section for more details.
 

Definition at line 30 of file PhastCons.pm.

Available Methods

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 void fetch_input ()
public free_aligned_sequence ()
public get_params ()
public go_figure_dbc ()
public void info ()
public input_id ()
public
Bio::EnsEMBL::Hive::AnalysisJob 
input_job ()
public new ()
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 root_id ()
public void run ()
public Arrayref runnable ()
public Array stack_trace ()
public String stack_trace_dump ()
public strict_hash_format ()
public void throw ()
public tree_file ()
public Depend try ()
public Int verbose ()
public warning ()
public worker ()
public worker_temp_directory ()
public Boolean write_output ()

Method Documentation

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

Undocumented method

public void Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::PhastCons::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::Production::GenomicAlignBlock::PhastCons::free_aligned_sequence ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::PhastCons::get_params ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::PhastCons::options ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::PhastCons::param_file ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::PhastCons::param_file_tmp ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::PhastCons::program ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::PhastCons::program_file ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::PhastCons::program_version ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::PhastCons::root_id ( )

Undocumented method

Code:
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public void Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::PhastCons::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::Production::GenomicAlignBlock::PhastCons::tree_file ( )

Undocumented method

Code:
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public Boolean Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::PhastCons::write_output ( )
    Title   :   write_output
    Usage   :   $self->write_output
    Function:   Write results to the database
    Returns :   1
    Args    :   none
 
Code:
click to view

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


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