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Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::BlastAndParsePAF Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::BlastAndParsePAF:

List of all members.


Class Summary

Synopsis

Description

Create fasta file containing batch_size number of sequences. Run ncbi_blastp and parse the output into
PeptideAlignFeature objects. Store PeptideAlignFeature objects in the compara database
Supported keys:
    'blast_param' => <string>
        ncbi blastp parameters
eg "-num_alignments 20 -seg 'yes' -best_hit_overhang 0.2 -best_hit_score_edge 0.1 -use_sw_tback"
    'fasta_dir' => <directory path>
        Path to fasta files
    'mlss_id' => <number>
        Method link species set id for Pecan. Obligatory
    'genome_db_id' => <number>
        Species genome db id.
    'offset' => <number>
        Offset into ordered array of member_ids. Obligatory
    'subset_id' => <number>
        Subset id of members to select
    'start_member_id' => <number>
        Member id of member at 'offset' in order array of member ids. Obligatory
    'batch_size' => <number>
        Number of members to write to fasta file
    'reuse_ss_id' => <number>
        Reuse species set id. Normally stored in the meta table. Obligatory.
    'do_transactions' => <0|1>
        Whether to do transactions. Default is yes.
 

Definition at line 44 of file BlastAndParsePAF.pm.

Available Methods

protected _write_output ()
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 fetch_input ()
public get_table_name_from_dbID ()
public go_figure_compara_dba ()
public go_figure_dbc ()
public void info ()
public input_id ()
public
Bio::EnsEMBL::Hive::AnalysisJob 
input_job ()
public load_members_from_db ()
public load_name2index_mapping_from_db ()
public load_name2index_mapping_from_file ()
public load_name2member_mapping_from_db ()
public name2index ()
public name2member ()
public new ()
public Array output ()
public pafs_equal ()
public param ()
public param_defaults ()
public param_substitute ()
public parameters ()
public parse_blast_table_into_paf ()
public Bio::EnsEMBL::Hive::Queen queen ()
public run ()
public Arrayref runnable ()
public sort_by_score_evalue_and_pid ()
public Array stack_trace ()
public String stack_trace_dump ()
public strict_hash_format ()
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::RunnableDB::MercatorPecan::BlastAndParsePAF::_write_output ( )

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::MercatorPecan::BlastAndParsePAF::fetch_input ( )

Undocumented method

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

public Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::BlastAndParsePAF::get_table_name_from_dbID ( )

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::MercatorPecan::BlastAndParsePAF::load_members_from_db ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::BlastAndParsePAF::load_name2index_mapping_from_db ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::BlastAndParsePAF::load_name2index_mapping_from_file ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::BlastAndParsePAF::load_name2member_mapping_from_db ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::BlastAndParsePAF::name2index ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::BlastAndParsePAF::name2member ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::BlastAndParsePAF::pafs_equal ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::BlastAndParsePAF::parse_blast_table_into_paf ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::BlastAndParsePAF::run ( )

Undocumented method

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

public Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::BlastAndParsePAF::sort_by_score_evalue_and_pid ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::BlastAndParsePAF::write_output ( )

Undocumented method

Code:
click to view

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


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