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Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::MCoffee Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::MCoffee:

List of all members.


Class Summary

Description

This Analysis/RunnableDB is designed to take a protein_tree cluster as input
Run an MCOFFEE multiple alignment on it, and store the resulting alignment
back into the protein_tree_member and protein_tree_member_score table.
input_id/parameters format eg: "{'protein_tree_id'=\>726093}"
    protein_tree_id       : use family_id to run multiple alignment on its members
    options               : commandline options to pass to the 'mcoffee' program
 

Synopsis

my $db     = Bio::EnsEMBL::Compara::DBAdaptor-\>new($locator);
my $mcoffee = Bio::EnsEMBL::Compara::RunnableDB::Mcoffee-\>new (
                                                    -db      =\> $db,
                                                    -input_id   =\> $input_id,
                                                    -analysis   =\> $analysis );
$mcoffee-\>fetch_input(); #reads from DB
$mcoffee-\>run();
$mcoffee-\>output();
$mcoffee-\>write_output(); #writes to DB

Definition at line 38 of file MCoffee.pm.

Available Methods

protected _get_alternate_alignment_tree ()
protected _store_aln_tags ()
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 dumpProteinTreeToWorkdir ()
public void 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 parse_and_store_alignment_into_proteintree ()
public Bio::EnsEMBL::Hive::Queen queen ()
public void run ()
public run_mcoffee ()
public Arrayref runnable ()
public Array stack_trace ()
public String stack_trace_dump ()
public strict_hash_format ()
public void throw ()
public Depend try ()
public update_single_peptide_tree ()
public Int verbose ()
public warning ()
public worker ()
public worker_temp_directory ()
public void write_output ()

Method Documentation

protected Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::MCoffee::_get_alternate_alignment_tree ( )

Undocumented method

Code:
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protected Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::MCoffee::_store_aln_tags ( )

Undocumented method

Code:
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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 Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::MCoffee::DESTROY ( )

Undocumented method

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

public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::MCoffee::dumpProteinTreeToWorkdir ( )

Undocumented method

Code:
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public void Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::MCoffee::fetch_input ( )
    Title   :   fetch_input
    Usage   :   $self->fetch_input
    Function:   Fetches input data for mcoffee from the database
    Returns :   none
    Args    :   none
 
Code:
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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::ProteinTrees::MCoffee::param_defaults ( )

Undocumented method

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

public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::MCoffee::parse_and_store_alignment_into_proteintree ( )

Undocumented method

Code:
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public void Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::MCoffee::run ( )
    Title   :   run
    Usage   :   $self->run
    Function:   runs MCOFFEE
    Returns :   none
    Args    :   none
 
Code:
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Reimplemented from Bio::EnsEMBL::Hive::Process.

public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::MCoffee::run_mcoffee ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::MCoffee::update_single_peptide_tree ( )

Undocumented method

Code:
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public void Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::MCoffee::write_output ( )
    Title   :   write_output
    Usage   :   $self->write_output
    Function:   parse mcoffee output and update protein_tree_member tables
    Returns :   none
    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/RunnableDB/ProteinTrees/MCoffee.pm