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

List of all members.


Class Summary

Synopsis

  my $db      = Bio::EnsEMBL::DBAdaptor-\>new($locator);
  my $genscan = Bio::EnsEMBL::Compara::Production::GenomicAlign::AlignmentNets-\>new (
                                                    -db      =\> $db,
                                                    -input_id   =\> $input_id
                                                    -analysis   =\> $analysis );
  $genscan-\>fetch_input();
  $genscan-\>run();
  $genscan-\>write_output(); #writes to DB

Description

Given an compara MethodLinkSpeciesSet identifer, and a reference genomic
slice identifer, fetches the GenomicAlignBlocks from the given compara
database, infers chains from the group identifiers, and then forms
an alignment net from the chains and writes the result
back to the database.
This module (at least for now) relies heavily on Jim Kent\'s Axt tools.
 

Definition at line 35 of file AlignmentNets.pm.

Available Methods

protected _write_output ()
public Bio::EnsEMBL::Analysis analysis ()
public BIN_DIR ()
public catch ()
public void check_if_exit_cleanly ()
public cleanse_output ()
public compara_cigars_from_daf_cigar ()
public compara_dba ()
public convert_output ()
public daf_cigar_from_compara_cigars ()
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 delete_alignments ()
public void deprecate ()
public DESTROY ()
public do_transactions ()
public Nothing fetch_input ()
public get_params ()
public go_figure_dbc ()
public void info ()
public input_id ()
public
Bio::EnsEMBL::Hive::AnalysisJob 
input_job ()
public INPUT_METHOD_LINK_TYPE ()
public MAX_GAP ()
public METHOD_LINK_SPECIES_SET_ID ()
public MIN_CHAIN_SCORE ()
public new ()
public output ()
public OUTPUT_METHOD_LINK_TYPE ()
public output_MethodLinkSpeciesSet ()
public param ()
public param_defaults ()
public param_substitute ()
public parameters ()
public Bio::EnsEMBL::Hive::Queen queen ()
public query_dnafrag ()
public query_DnaFrag_hash ()
public REGION_END ()
public REGION_START ()
public run ()
public Arrayref runnable ()
public sort_chains_by_max_block_score ()
public split_feature ()
public Array stack_trace ()
public String stack_trace_dump ()
public strict_hash_format ()
public target_DnaFrag_hash ()
public void throw ()
public Depend try ()
public Int verbose ()
public warning ()
public worker ()
public worker_temp_directory ()
public write_output ()

Method Documentation

protected Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::AlignmentProcessing::_write_output ( ) [inherited]

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::AlignmentNets::BIN_DIR ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::AlignmentProcessing::cleanse_output ( ) [inherited]

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::AlignmentProcessing::compara_cigars_from_daf_cigar ( ) [inherited]

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::AlignmentProcessing::compara_dba ( ) [inherited]

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::AlignmentProcessing::convert_output ( ) [inherited]

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::AlignmentProcessing::daf_cigar_from_compara_cigars ( ) [inherited]

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::AlignmentNets::delete_alignments ( )

Undocumented method

Code:
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Reimplemented from Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::AlignmentProcessing.

public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::AlignmentProcessing::do_transactions ( ) [inherited]

Undocumented method

Code:
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public Nothing Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::AlignmentNets::fetch_input ( )
    Title   :   fetch_input
    Usage   :   $self->fetch_input
    Function:   
    Returns :   nothing
    Args    :   none
 
Code:
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Reimplemented from Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::AlignmentProcessing.

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

Undocumented method

Code:
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Reimplemented from Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::AlignmentProcessing.

public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::AlignmentProcessing::INPUT_METHOD_LINK_TYPE ( ) [inherited]

Undocumented method

public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::AlignmentProcessing::MAX_GAP ( ) [inherited]

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::AlignmentNets::METHOD_LINK_SPECIES_SET_ID ( )

Undocumented method

public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::AlignmentProcessing::MIN_CHAIN_SCORE ( ) [inherited]

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::AlignmentProcessing::new ( ) [inherited]

Undocumented method

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

public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::AlignmentProcessing::output ( ) [inherited]

Undocumented method

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

public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::AlignmentProcessing::OUTPUT_METHOD_LINK_TYPE ( ) [inherited]

Undocumented method

public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::AlignmentProcessing::output_MethodLinkSpeciesSet ( ) [inherited]

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::AlignmentNets::query_dnafrag ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::AlignmentProcessing::query_DnaFrag_hash ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::AlignmentNets::REGION_END ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::AlignmentNets::REGION_START ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::AlignmentNets::run ( )

Undocumented method

Code:
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Reimplemented from Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::AlignmentProcessing.

public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::AlignmentProcessing::sort_chains_by_max_block_score ( ) [inherited]

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::AlignmentProcessing::split_feature ( ) [inherited]

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::AlignmentProcessing::target_DnaFrag_hash ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::AlignmentNets::write_output ( )

Undocumented method

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Reimplemented from Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::AlignmentProcessing.


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