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

List of all members.


Class Summary

Description

This Analysis/RunnableDB is designed to take ProteinTree as input.
This must already have a multiple alignment run on it. It uses that
alignment as input into the QuickTree program which then generates a
simple phylogenetic tree to be broken down into 2 pieces.
Google QuickTree to get the latest tar.gz from the Sanger.
Google sreformat to get the sequence reformatter that switches from fasta to stockholm.
input_id/parameters format eg: "{'protein_tree_id'=\>1234,'clusterset_id'=\>1}"
    protein_tree_id : use 'id' to fetch a cluster from the ProteinTree
 

Synopsis

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

Definition at line 46 of file QuickTreeBreak.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 dumpTreeMultipleAlignmentToWorkdir ()
public void fetch_input ()
public generate_subtrees ()
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 release_tree ()
public void run ()
public run_quicktreebreak ()
public Arrayref runnable ()
public Array stack_trace ()
public String stack_trace_dump ()
public store_clusters ()
public store_proteintrees ()
public strict_hash_format ()
public void throw ()
public Depend try ()
public Int verbose ()
public warning ()
public worker ()
public worker_temp_directory ()
public void 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:
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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::QuickTreeBreak::DESTROY ( )

Undocumented method

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

public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::QuickTreeBreak::dumpTreeMultipleAlignmentToWorkdir ( )

Undocumented method

Code:
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public void Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::QuickTreeBreak::fetch_input ( )
    Title   :   fetch_input
    Usage   :   $self->fetch_input
    Function:   Fetches input data for repeatmasker from the database
    Returns :   none
    Args    :   none
 
Code:
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Reimplemented from Bio::EnsEMBL::Hive::Process.

public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::QuickTreeBreak::generate_subtrees ( )

Undocumented method

Code:
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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.
 
Code:
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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::QuickTreeBreak::release_tree ( )

Undocumented method

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

public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::QuickTreeBreak::run_quicktreebreak ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::QuickTreeBreak::store_clusters ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::QuickTreeBreak::store_proteintrees ( )

Undocumented method

Code:
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public void Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::QuickTreeBreak::write_output ( )
    Title   :   write_output
    Usage   :   $self->write_output
    Function:   stores proteintree
    Returns :   none
    Args    :   none
 
Code:
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Reimplemented from Bio::EnsEMBL::Hive::Process.


The documentation for this class was generated from the following file: