ensembl-hive
2.6
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Public Member Functions | |
public void | analyse () |
public void | classify_source_genes_by_type () |
public void | classify_genes_by_mapping_simple () |
public void | classify_genes_by_mapping () |
public String | add () |
public String | get () |
public Arrayref | get_all_by_subclass () |
public Arrayref | get_all_by_class () |
public Int | get_count_by_subclass () |
public Int | get_count_by_class () |
public Arrayref | get_all_classes () |
public String | class_key () |
public void | write_results_to_file () |
public void | create_clicklist () |
public void | create_mapping_summary () |
public String | read_from_file () |
Public Member Functions inherited from Bio::EnsEMBL::IdMapping::BaseObject | |
public $this | new () |
public Filehandle | get_filehandle () |
public Boolean | file_exists () |
public SQLStatement | fetch_value_from_db () |
public Int | dump_table_to_file () |
public Int | upload_file_into_table () |
public Bio::EnsEMBL::Utils::Logger | logger () |
public Bio::EnsEMBL::Utils::ConfParser | conf () |
public Bio::EnsEMBL::IdMapping::Cache | cache () |
This is a utility module which analyses the stable Id mapping results by providing various sorts of mapping statistics. It also creates clicklists and a mapping summary.
Definition at line 38 of file ResultAnalyser.pm.
public String Bio::EnsEMBL::IdMapping::ResultAnalyser::add | ( | ) |
Arg[1] : String $dbtype - db type ('source' or 'target') Arg[2] : String $class - key identifying a gene type (see class_key()) Arg[3] : String $subclass - status identifier (e.g. 'mapped', 'lost') Arg[4] : String $stable_id - gene stable Id Arg[5] : String $val - value (usually 0 or 1) Example :
Description : Add a stable Id / property pair to a name/dbtype lookup hash.
The datastructure is a bit of a bloat, but is general enough to be used as a lookup hash and to generate statistics (counts by type) and debug lists (dump by type). Return type : String - the added value Exceptions : none Caller : internal Status : At Risk : under development
public void Bio::EnsEMBL::IdMapping::ResultAnalyser::analyse | ( | ) |
Arg[1] : Bio::EnsEMBL::IdMapping::MappingList $gene_mappings - the gene mappings to analyse Arg[2] : Arrayref of Strings - similarity events Example :
Description : Analyses the results of a stable Id mapping run. Return type : none Exceptions : thrown on wrong or missing arguments Caller : general Status : At Risk : under development
public String Bio::EnsEMBL::IdMapping::ResultAnalyser::class_key | ( | ) |
Arg[1] : Bio::EnsEMBL::IdMapping::TinyGene $gene - a gene object Example :
Description : Generates a key identifying a gene class. This identifier is composed from the gene's logic naame, and biotye. Return type : String Exceptions : none Caller : internal Status : At Risk : under development
public void Bio::EnsEMBL::IdMapping::ResultAnalyser::classify_genes_by_mapping | ( | ) |
Arg[1] : Bio::EnsEMBL::IdMapping::MapppingList $gene_mappings - gene mappings to classify Arg[2] : Arrayref of Strings - similarity events Example :
Description : Classifies genes by mapping. Status is 'mapped' => stable Id was mapped 'lost_similar' => stable Id not mapped, but there is a similarity entry for the source Id 'lost_definite' => not mapped and no similarity Return type : none Exceptions : thrown on wrong or missing argument Caller : This method is not in use at the momen. Status : At Risk : under development
public void Bio::EnsEMBL::IdMapping::ResultAnalyser::classify_genes_by_mapping_simple | ( | ) |
Arg[1] : Bio::EnsEMBL::IdMapping::MapppingList $gene_mappings - gene mappings to classify Example :
Description : Classifies target genes by mapping ('mapped' or 'unmapped'). Return type : none Exceptions : thrown on wrong or missing argument Caller : This method is not in use at the momen. Status : At Risk : under development
public void Bio::EnsEMBL::IdMapping::ResultAnalyser::classify_source_genes_by_type | ( | ) |
Example :
Description : Classifies source genes by type and adds them to the internal datastructure. For the format of the classification string see class_key(). Return type : none Exceptions : none Caller : internal Status : At Risk : under development
public void Bio::EnsEMBL::IdMapping::ResultAnalyser::create_clicklist | ( | ) |
Example :
Description : Writes an html file which contains a list of all lost genes, with hyperlinks to the appropriate archive website. This is to manually check lost genes. Return type : none Exceptions : none Caller : general Status : At Risk : under development
public void Bio::EnsEMBL::IdMapping::ResultAnalyser::create_mapping_summary | ( | ) |
Example :
Description : Writes a text file containing a summary of the mapping stats. This will be emailed to the genebuilder for evaluation (you will have to manually send the email, using the text in "mapping_summary.txt" as the template). Return type : none Exceptions : none Caller : general Status : At Risk : under development
public String Bio::EnsEMBL::IdMapping::ResultAnalyser::get | ( | ) |
Arg[1] : String $dbtype - db type ('source' or 'target') Arg[2] : String $class - key identifying a gene type (see class_key()) Arg[3] : String $subclass - status identifier (e.g. 'mapped', 'lost') Arg[4] : String $stable_id - gene stable Id Example :
Description : Gets a stable Id mapping status from the internal datastructure. Return type : String Exceptions : none Caller : internal Status : At Risk : under development
public Arrayref Bio::EnsEMBL::IdMapping::ResultAnalyser::get_all_by_class | ( | ) |
Arg[1] : String $dbtype - db type ('source' or 'target') Arg[2] : String $class - key identifying a gene type (see class_key()) Example :
Description : Gets a list of stable Id for a given class. Return type : Arrayref of String (stable Ids) Exceptions : thrown on missing arguments Caller : internal Status : At Risk : under development
public Arrayref Bio::EnsEMBL::IdMapping::ResultAnalyser::get_all_by_subclass | ( | ) |
Arg[1] : String $dbtype - db type ('source' or 'target') Arg[2] : String $class - key identifying a gene type (see class_key()) Arg[3] : String $subclass - status identifier (e.g. 'mapped', 'lost') Example :
Description : Gets a list of stable Id for a given subclass. Return type : Arrayref of String (stable Ids) Exceptions : thrown on missing arguments Caller : internal Status : At Risk : under development
public Arrayref Bio::EnsEMBL::IdMapping::ResultAnalyser::get_all_classes | ( | ) |
Arg[1] : String $dbtype - db type ('source' or 'target') Example :
Description : Gets a list of classes in the ResultAnalyser. Return type : Arrayref of String Exceptions : thrown on missing argument Caller : internal Status : At Risk : under development
public Int Bio::EnsEMBL::IdMapping::ResultAnalyser::get_count_by_class | ( | ) |
Arg[1] : String $dbtype - db type ('source' or 'target') Arg[2] : String $class - key identifying a gene type (see class_key()) Example :
Description : Gets the number of stable Ids for a given class. Return type : Int Exceptions : thrown on missing arguments Caller : internal Status : At Risk : under development
public Int Bio::EnsEMBL::IdMapping::ResultAnalyser::get_count_by_subclass | ( | ) |
Arg[1] : String $dbtype - db type ('source' or 'target') Arg[2] : String $class - key identifying a gene type (see class_key()) Arg[3] : String $subclass - status identifier (e.g. 'mapped', 'lost') Example :
Description : Gets the number of stable Ids for a given subclass. Return type : Int Exceptions : thrown on missing arguments Caller : internal Status : At Risk : under development
public String Bio::EnsEMBL::IdMapping::ResultAnalyser::read_from_file | ( | ) |
Arg[1] : String $filename - name of file to read Arg[2] : (optional) String $append - directory name to append to basedir Example :
Description : Reads mapping stats from a file. Return type : String Exceptions : none Caller : internal Status : At Risk : under development
public void Bio::EnsEMBL::IdMapping::ResultAnalyser::write_results_to_file | ( | ) |
Example :
Description : Writes the results of the result analysis to a file. This is a human-readable text detailing the mapping statistics. Return type : none Exceptions : none Caller : general Status : At Risk : under development