Bio::EnsEMBL::MetaData::AnnotationAnalyzer Class Reference

List of all members.

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Class Summary

Synopsis

my $anal = Bio::EnsEMBL::MetaData::AnnotationAnalyzer->new();
my $details = $anal->analyze_annotation($dba);

Description

Utility class for counting xrefs, variations etc. associated with a genome

Definition at line 21 of file AnnotationAnalyzer.pm.

Available Methods
public Hash	analyze_alignments ()
public Hash	analyze_annotation ()
public Hash	analyze_compara ()
public Hash	analyze_features ()
public Hash	analyze_tracks ()
public Hash	analyze_variation ()
public Int	count_by_biotype ()
public Int	count_by_interpro ()
public Int	count_by_xref ()
public Hashref	count_features ()
public Hashref	count_genotypes ()
public Int	count_interpro ()
public Int	count_interpro_domains ()
public Int	count_phenotypes ()
public Hashref	count_structural_variations ()
public Int	count_toplevel ()
public Hashref	count_variations ()
public Int	count_xrefs ()
public	new ()

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Method Documentation

public Hash Bio::EnsEMBL::MetaData::AnnotationAnalyzer::analyze_alignments

(

)

  Arg        : Bio::EnsEMBL::DBSQL::DBAdaptor
  Description: Analyzes alignments for sequences to the assembly 
  Returntype : Hash ref - keys are source_type (e.g. RNA seq), values are arrayrefs of hashrefs containing track details (source_name,description,source_url)
  Exceptions : none
  Caller     : general
  Status     : Stable
 

Code:

public Hash Bio::EnsEMBL::MetaData::AnnotationAnalyzer::analyze_annotation

(

)

  Arg        : Bio::EnsEMBL::DBSQL::DBAdaptor
  Description: Analyzes annotation content of the supplied core DB
  Returntype : 	Hash ref with the following keys:
					nProteinCoding - number of protein coding genes
					nProteinCodingUniProtKBSwissProt - number of protein coding genes with at least one SwissPROT entry
					nProteinCodingUniProtKBTrEMBL - number of protein coding genes with at least one TrEMBL entry
					nProteinCodingGO - number of protein coding genes with at least one GO term
					nProteinCodingInterPro - number of protein coding genes with at least one InterPro match
					nUniProtKBSwissProt - number of distinct UniProtKB/TrEMBL entries matching at least one translation
					nUniProtKBTrEMBL - number of distinct UniProtKB/TrEMBL entries matching at least one translation
					nGO - number of distinct GO terms matching at least one translation
					nInterPro - number of distinct InterPro entries matching at least one feature
					nInterProDomains - number of distinct protein features matching an InterPro domains
  Exceptions : none
  Caller     : general
  Status     : Stable
 

Code:

public Hash Bio::EnsEMBL::MetaData::AnnotationAnalyzer::analyze_compara

(

)

  Arg        : Bio::EnsEMBL::DBSQL::DBAdaptor
  Arg        : Bio::EnsEMBL::Compara::DBSQL::DBAdaptor
  Description: Analyzes compara methods found in the supplied compara database involving the supplied core species
  Returntype : 	Hash ref (keys are method names, values are arrays of partner species)
  Exceptions : none
  Caller     : general
  Status     : Stable
 

Code:

public Hash Bio::EnsEMBL::MetaData::AnnotationAnalyzer::analyze_features

(

)

  Arg        : Bio::EnsEMBL::DBSQL::DBAdaptor
  Description: Analyzes features found in the supplied core/otherfeatures database (simple_feature,repeat_feature,protein_align_feature,dna_align_features)
  Returntype : 	Hash ref (keys are feature tables, values are hashrefs of count by analysis name)
  Exceptions : none
  Caller     : general
  Status     : Stable
 

Code:

public Hash Bio::EnsEMBL::MetaData::AnnotationAnalyzer::analyze_tracks

(

)

  Arg        : Bio::EnsEMBL::DBSQL::DBAdaptor
  Description: Analyzes tracks attached to the supplied core database
  Returntype : Hash ref - keys are source_type (e.g. RNA seq), values are arrayrefs of hashrefs containing track details (source_name,description,source_url)
  Exceptions : none
  Caller     : general
  Status     : Stable	
 

Code:

public Hash Bio::EnsEMBL::MetaData::AnnotationAnalyzer::analyze_variation

(

)

  Arg        : Bio::EnsEMBL::Variation::DBSQL::DBAdaptor
  Description: Analyzes variation found in the supplied variation database
  Returntype : 	Hash ref with the following keys
					variations - count of variations per source
					structuralVariations - count of structural variations per source
					genotypes - count of genotypes per sample
					phenotypes - count of variation annotations per phenotype
  Exceptions : none
  Caller     : general
  Status     : Stable
 

Code:

public Int Bio::EnsEMBL::MetaData::AnnotationAnalyzer::count_by_biotype

(

)

  Arg        : Bio::EnsEMBL::DBSQL::DBAdaptor
  Arg        : String (biotype)
  Description: Returns count of genes with specified biotype
  Returntype : Integer
  Exceptions : none
  Caller     : internal
  Status     : Stable
 

Code:

public Int Bio::EnsEMBL::MetaData::AnnotationAnalyzer::count_by_interpro

(

)

  Arg        : Bio::EnsEMBL::DBSQL::DBAdaptor
  Description: Returns count of genes with InterPro domains
  Returntype : Integer
  Exceptions : none
  Caller     : internal
  Status     : Stable
 

Code:

public Int Bio::EnsEMBL::MetaData::AnnotationAnalyzer::count_by_xref

(

)

  Arg        : Bio::EnsEMBL::DBSQL::DBAdaptor
  Arg        : Arrayref of dbnames 
  Arg        : (optional) String (biotype)
  Description: Returns count of genes with specified cross-reference
  Returntype : Integer
  Exceptions : none
  Caller     : internal
  Status     : Stable
 

Code:

public Hashref Bio::EnsEMBL::MetaData::AnnotationAnalyzer::count_features

(

)

  Arg        : Bio::EnsEMBL::DBSQL::DBAdaptor
  Arg        : String - feature type (e.g. RepeatFeature)
  Description: Returns count of specified feature by analysis
  Returntype : Hashref
  Exceptions : none
  Caller     : internal
  Status     : Stable
 

Code:

public Hashref Bio::EnsEMBL::MetaData::AnnotationAnalyzer::count_genotypes

(

)

  Arg        : Bio::EnsEMBL::Variation::DBSQL::DBAdaptor
  Description: Returns count of genotypes by source
  Returntype : Hashref
  Exceptions : none
  Caller     : internal
  Status     : Stable
 

Code:

public Int Bio::EnsEMBL::MetaData::AnnotationAnalyzer::count_interpro

(

)

  Arg        : Bio::EnsEMBL::DBSQL::DBAdaptor
  Description: Returns count of InterPro cross-references
  Returntype : Integer
  Exceptions : none
  Caller     : internal
  Status     : Stable
 

Code:

public Int Bio::EnsEMBL::MetaData::AnnotationAnalyzer::count_interpro_domains

(

)

  Arg        : Bio::EnsEMBL::DBSQL::DBAdaptor
  Description: Returns count of InterPro domains
  Returntype : Integer
  Exceptions : none
  Caller     : internal
  Status     : Stable
 

Code:

public Int Bio::EnsEMBL::MetaData::AnnotationAnalyzer::count_phenotypes

(

)

  Arg        : Bio::EnsEMBL::Variation::DBSQL::DBAdaptor
  Description: Returns count of phenotypes by name
  Returntype : Integer
  Exceptions : none
  Caller     : internal
  Status     : Stable
 

Code:

public Hashref Bio::EnsEMBL::MetaData::AnnotationAnalyzer::count_structural_variations

(

)

  Arg        : Bio::EnsEMBL::Variation::DBSQL::DBAdaptor
  Description: Returns count of structural variations by source
  Returntype : Hashref
  Exceptions : none
  Caller     : internal
  Status     : Stable
 

Code:

public Int Bio::EnsEMBL::MetaData::AnnotationAnalyzer::count_toplevel

(

)

  Arg        : Bio::EnsEMBL::DBSQL::DBAdaptor
  Description: Returns count of top-level regions
  Returntype : Integer
  Exceptions : none
  Caller     : internal
  Status     : Stable
 

Code:

public Hashref Bio::EnsEMBL::MetaData::AnnotationAnalyzer::count_variations

(

)

  Arg        : Bio::EnsEMBL::Variation::DBSQL::DBAdaptor
  Description: Returns count of variations by source
  Returntype : Hashref
  Exceptions : none
  Caller     : internal
  Status     : Stable
 

Code:

public Int Bio::EnsEMBL::MetaData::AnnotationAnalyzer::count_xrefs

(

)

  Arg        : Bio::EnsEMBL::DBSQL::DBAdaptor
  Arg        : One or more dbnames
  Description: Returns count of numbers of cross-references to supplied database(s)
  Returntype : Integer
  Exceptions : none
  Caller     : internal
  Status     : Stable
 

Code:

public Bio::EnsEMBL::MetaData::AnnotationAnalyzer::new

(

)

Undocumented method

Code:

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

• Bio/EnsEMBL/MetaData/AnnotationAnalyzer.pm