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Bio::EnsEMBL::IdMapping::ExonScoreBuilder Class Reference
Inheritance diagram for Bio::EnsEMBL::IdMapping::ExonScoreBuilder:

List of all members.


Class Summary

Synopsis

Description

Combines ExonScoreBuilder, ExonDirectMapper and ExonerateRunner from
Java application.
 

Definition at line 19 of file ExonScoreBuilder.pm.

Available Methods

public build_overlap_scores ()
public
Bio::EnsEMBL::IdMapping::Cache 
cache ()
public calc_overlap_score ()
public compare_exon_containers ()
public
Bio::EnsEMBL::Utils::ConfParser 
conf ()
public
Bio::EnsEMBL::IdMapping::ScoredMappingMatrix 
create_shrinked_matrix ()
public dump_filtered_exons ()
public Int dump_table_to_file ()
public exon_fasta_file ()
public exonerate_score ()
public SQLStatement fetch_value_from_db ()
public Boolean file_exists ()
public Filehandle get_filehandle ()
public void internal_id_rescore ()
public void log_matrix_stats ()
public Bio::EnsEMBL::Utils::Logger logger ()
public $this new ()
public non_mapped_transcript_rescore ()
public overlap_score ()
public parse_exonerate_results ()
public run_exonerate ()
public score_exons ()
public sort_exons ()
public Int upload_file_into_table ()
public write_filtered_exons ()

Method Documentation

public Bio::EnsEMBL::IdMapping::ExonScoreBuilder::build_overlap_scores ( )

Undocumented method

Code:
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public Bio::EnsEMBL::IdMapping::Cache Bio::EnsEMBL::IdMapping::BaseObject::cache ( ) [inherited]
  Arg[1]      : (optional) Bio::EnsEMBL::IdMapping::Cache - the cache to set
  Example     : $object->cache->read_from_file('source');
  Description : Getter/setter for cache object
  Return type : Bio::EnsEMBL::IdMapping::Cache
  Exceptions  : none
  Caller      : constructor
  Status      : At Risk
              : under development
 
Code:
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public Bio::EnsEMBL::IdMapping::ExonScoreBuilder::calc_overlap_score ( )

Undocumented method

Code:
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public Bio::EnsEMBL::IdMapping::ExonScoreBuilder::compare_exon_containers ( )

Undocumented method

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public Bio::EnsEMBL::Utils::ConfParser Bio::EnsEMBL::IdMapping::BaseObject::conf ( ) [inherited]
  Arg[1]      : (optional) Bio::EnsEMBL::Utils::ConfParser - the configuration
                to set
  Example     : my $basedir = $object->conf->param('basedir');
  Description : Getter/setter for configuration object
  Return type : Bio::EnsEMBL::Utils::ConfParser
  Exceptions  : none
  Caller      : constructor
  Status      : At Risk
              : under development
 
Code:
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public Bio::EnsEMBL::IdMapping::ScoredMappingMatrix Bio::EnsEMBL::IdMapping::ScoreBuilder::create_shrinked_matrix ( ) [inherited]
  Arg[1]      : Bio::EnsEMBL::Idmapping::ScoredMappingMatrix $matrix - a scoring
                matrix
  Arg[2]      : Bio::EnsEMBL::Idmapping::MappingList $mappings - mappings
  Arg[3]      : String $cache_file - base name of a cache file (extension '.ser'
                will be added automatically) for the returned matrix
  Example     : my $new_scores = $score_builder->create_shrinked_matrix(
                  $gene_scores, $mappings, "gene_matrix1");
  Description : Create a shrinked scoring matrix which doesn't contain entries
                which were already mapped. It also logs how many new mappings
                were added in this process.
  Return type : Bio::EnsEMBL::IdMapping::ScoredMappingMatrix
  Exceptions  : thrown on wrong or missing arguments
  Caller      : InternalIdMapper plugin
  Status      : At Risk
              : under development
 
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public Bio::EnsEMBL::IdMapping::ExonScoreBuilder::dump_filtered_exons ( )

Undocumented method

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public Int Bio::EnsEMBL::IdMapping::BaseObject::dump_table_to_file ( ) [inherited]
  Arg[1]      : String $dbtype - db type (source|target)
  Arg[2]      : String $table - name of table to dump
  Arg[3]      : String $filename - name of dump file
  Arg[4]      : Boolean $check_existing - turn on test for existing dump
  Example     : my $rows_dumped = $object->dump_table_to_file('source',
                  'stable_id_event', 'stable_id_event_existing.txt');
  Description : Dumps the contents of a db table to a tab-delimited file. The
                dump file will be written to a subdirectory called 'tables'
                under the basedir from your configuration.
  Return type : Int - the number of rows dumped
  Exceptions  : thrown on wrong or missing arguments
  Caller      : general
  Status      : At Risk
              : under development
 
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public Bio::EnsEMBL::IdMapping::ExonScoreBuilder::exon_fasta_file ( )

Undocumented method

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public Bio::EnsEMBL::IdMapping::ExonScoreBuilder::exonerate_score ( )

Undocumented method

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public SQLStatement Bio::EnsEMBL::IdMapping::BaseObject::fetch_value_from_db ( ) [inherited]
  Arg[1]      : DBI::db $dbh - a DBI database handle
  Arg[2]      : String $sql - SQL statement to execute
  Example     : my $num_genes = $object->fetch_value_from_db($dbh,
                  'SELECT count(*) FROM gene');
  Description : Executes an SQL statement on a db handle and returns the first
                column of the first row returned. Useful for queries returning a
                single value, like table counts.
  Return type : Return type of SQL statement
  Exceptions  : thrown on wrong or missing arguments
  Caller      : general
  Status      : At Risk
              : under development
 
Code:
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public Boolean Bio::EnsEMBL::IdMapping::BaseObject::file_exists ( ) [inherited]
  Arg[1]      : String $filename - filename to test
  Arg[2]      : Boolean $path_append - turn on pre-pending of basedir
  Example     : unless ($object->file_exists('gene_mappings.ser', 1)) {
                  $object->do_gene_mapping;
                }
  Description : Tests if a file exists and has non-zero size.
  Return type : Boolean
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
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public Filehandle Bio::EnsEMBL::IdMapping::BaseObject::get_filehandle ( ) [inherited]
  Arg[1]      : String $filename - filename for filehandle
  Arg[2]      : String $path_append - append subdirectory name to basedir
  Arg[3]      : String $mode - filehandle mode (<|>|>>)
  Example     : my $fh = $object->get_filehandle('mapping_stats.txt', 'stats',
                  '>');
                print $fh "Stats:\\n";
  Description : Returns a filehandle to a file for reading or writing. The file
                is qualified with the basedir defined in the configuration and
                an optional subdirectory name.
  Return type : filehandle
  Exceptions  : thrown on missing filename
  Caller      : general
  Status      : At Risk
              : under development
 
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public void Bio::EnsEMBL::IdMapping::ScoreBuilder::internal_id_rescore ( ) [inherited]
  Arg[1]      : Bio::EnsEMBL::Idmapping::ScoredMappingMatrix $matrix - a scoring
                matrix
  Example     : $score_builder->internal_id_rescore($gene_scores);
  Description : Rescore ambiguous mappings based on internal Ids. This is the
                last disambiguation step and is only useful if objects with the
                same internal Id were used in source and target dbs (e.g. in
                patch builds or if objects were copied from source to target).
                If a source and target gene have the same internal Id and there
                are mappings to other target genes then these *other* mappings
                are penalised.
  Return type : none
  Exceptions  : thrown on wrong or missing argument
  Caller      : InternalIdMapper plugins
  Status      : At Risk
              : under development
 
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public void Bio::EnsEMBL::IdMapping::ScoreBuilder::log_matrix_stats ( ) [inherited]
  Arg[1]      : Bio::EnsEMBL::Idmapping::ScoredMappingMatrix $matrix - a scoring
                matrix
  Example     : $score_builder->log_matrix_stats;
  Description : Logs scoring matrix statistics (number of entries, min/max/avg
                scores).
  Return type : none
  Exceptions  : thrown on wrong or missing argument
  Caller      : general
  Status      : At Risk
              : under development
 
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public Bio::EnsEMBL::Utils::Logger Bio::EnsEMBL::IdMapping::BaseObject::logger ( ) [inherited]
  Arg[1]      : (optional) Bio::EnsEMBL::Utils::Logger - the logger to set
  Example     : $object->logger->info("Starting ID mapping.\\n");
  Description : Getter/setter for logger object
  Return type : Bio::EnsEMBL::Utils::Logger
  Exceptions  : none
  Caller      : constructor
  Status      : At Risk
              : under development
 
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public $this Bio::EnsEMBL::IdMapping::BaseObject::new ( ) [inherited]
  Arg [LOGGER]: Bio::EnsEMBL::Utils::Logger $logger - a logger object
  Arg [CONF]  : Bio::EnsEMBL::Utils::ConfParser $conf - a configuration object
  Arg [CACHE] : Bio::EnsEMBL::IdMapping::Cache $cache - a cache object
  Example     : my $object = Bio::EnsEMBL::IdMapping::BaseObjectSubclass->new(
                  -LOGGER => $logger,
                  -CONF   => $conf,
                  -CACHE  => $cache
                );
  Description : Constructor
  Return type : implementing subclass type
  Exceptions  : thrown on wrong or missing arguments
  Caller      : general
  Status      : At Risk
              : under development
 
Code:
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Reimplemented in Bio::EnsEMBL::IdMapping::StableIdMapper.

public Bio::EnsEMBL::IdMapping::ExonScoreBuilder::non_mapped_transcript_rescore ( )

Undocumented method

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public Bio::EnsEMBL::IdMapping::ExonScoreBuilder::overlap_score ( )

Undocumented method

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public Bio::EnsEMBL::IdMapping::ExonScoreBuilder::parse_exonerate_results ( )

Undocumented method

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public Bio::EnsEMBL::IdMapping::ExonScoreBuilder::run_exonerate ( )

Undocumented method

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public Bio::EnsEMBL::IdMapping::ExonScoreBuilder::score_exons ( )

Undocumented method

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public Bio::EnsEMBL::IdMapping::ExonScoreBuilder::sort_exons ( )

Undocumented method

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public Int Bio::EnsEMBL::IdMapping::BaseObject::upload_file_into_table ( ) [inherited]
  Arg[1]      : String $dbtype - db type (source|target)
  Arg[2]      : String $table - name of table to upload the data to
  Arg[3]      : String $filename - name of dump file
  Arg[4]      : Boolean $no_check_empty - don't check if table is empty
  Example     : my $rows_uploaded = $object->upload_file_into_table('target',
                  'stable_id_event', 'stable_id_event_new.txt');
  Description : Uploads a tab-delimited data file into a db table. The data file
                will be taken from a subdirectory 'tables' under your configured
                basedir. If the db table isn't empty and $no_check_empty isn't
                set, no data is uploaded (and a warning is issued).
  Return type : Int - the number of rows uploaded
  Exceptions  : thrown on wrong or missing arguments
  Caller      : general
  Status      : At Risk
              : under development
 
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public Bio::EnsEMBL::IdMapping::ExonScoreBuilder::write_filtered_exons ( )

Undocumented method

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