class Bio::KEGG::ORTHOLOGY

Description¶ ↑

KO (KEGG Orthology) entry parser.

`References`¶ ↑

Constants

DELIMITER
TAGSIZE

Public Class Methods

Source

   # File lib/bio/db/kegg/orthology.rb
63 def initialize(entry)
64   super(entry, TAGSIZE)
65 end

Reads a flat file format entry of the KO database.

Calls superclass method Bio::NCBIDB::new

Public Instance Methods

dblinks ()

Alias for: dblinks_as_hash

dblinks_as_hash ()

Source

   # File lib/bio/db/kegg/orthology.rb
33 def dblinks_as_hash; super; end

Returns a Hash of the DB name and an Array of entry IDs in DBLINKS field.

Calls superclass method Bio::KEGG::Common::DblinksAsHash#dblinks_as_hash

Also aliased as: dblinks

dblinks_as_strings ()

Source

    # File lib/bio/db/kegg/orthology.rb
121 def dblinks_as_strings
122   lines_fetch('DBLINKS')
123 end

Returns an Array of a database name and entry IDs in DBLINKS field.

definition ()

Source

   # File lib/bio/db/kegg/orthology.rb
83 def definition
84   field_fetch('DEFINITION')
85 end

Returns DEFINITION field of the entry.

entry_id ()

Source

   # File lib/bio/db/kegg/orthology.rb
68 def entry_id
69   field_fetch('ENTRY')[/\S+/]
70 end

Returns ID of the entry.

genes ()

Alias for: genes_as_hash

genes_as_hash ()

Source

   # File lib/bio/db/kegg/orthology.rb
38 def genes_as_hash; super; end

Returns a Hash of the organism ID and an Array of entry IDs in GENES field.

Calls superclass method Bio::KEGG::Common::GenesAsHash#genes_as_hash

Also aliased as: genes

genes_as_strings ()

Source

    # File lib/bio/db/kegg/orthology.rb
126 def genes_as_strings
127   lines_fetch('GENES')
128 end

Returns an Array of the organism ID and entry IDs in GENES field.

keggclass ()

Source

   # File lib/bio/db/kegg/orthology.rb
88 def keggclass
89   field_fetch('CLASS')
90 end

Returns CLASS field of the entry.

keggclasses ()

Source

   # File lib/bio/db/kegg/orthology.rb
93 def keggclasses
94   keggclass.gsub(/ \[[^\]]+/, '').split(/\] ?/)
95 end

Returns an Array of biological classes in CLASS field.

modules ()

Alias for: modules_as_hash

modules_as_hash ()

Source

   # File lib/bio/db/kegg/orthology.rb
52 def modules_as_hash; super; end

Returns MODULE field as a Hash. Each key of the hash is KEGG MODULE ID, and each value is the name of the Pathway Module.

Returns: Hash

Calls superclass method Bio::KEGG::Common::ModulesAsHash#modules_as_hash

Also aliased as: modules

modules_as_strings ()

Source

    # File lib/bio/db/kegg/orthology.rb
116 def modules_as_strings
117   lines_fetch('MODULE')
118 end

Returns MODULE field of the entry.

Returns: Array containing String objects

name ()

Source

   # File lib/bio/db/kegg/orthology.rb
73 def name
74   field_fetch('NAME')
75 end

Returns NAME field of the entry.

names ()

Source

   # File lib/bio/db/kegg/orthology.rb
78 def names
79   name.split(', ')
80 end

Returns an Array of names in NAME field.

pathways ()

Alias for: pathways_as_hash

pathways_as_hash ()

Source

   # File lib/bio/db/kegg/orthology.rb
43 def pathways_as_hash; super; end

Returns a Hash of the pathway ID and name in PATHWAY field.

Calls superclass method Bio::KEGG::Common::PathwaysAsHash#pathways_as_hash

Also aliased as: pathways

pathways_as_strings ()

Source

    # File lib/bio/db/kegg/orthology.rb
100 def pathways_as_strings
101   lines_fetch('PATHWAY')
102 end

Pathways described in the PATHWAY field.

Returns: Array containing String

pathways_in_keggclass ()

Source

    # File lib/bio/db/kegg/orthology.rb
109 def pathways_in_keggclass
110   keggclass.scan(/\[PATH:(.*?)\]/).flatten
111 end

OBSOLETE Do not use this method. Because KEGG ORTHOLOGY format is changed and PATHWAY field is added, older “pathways” method is renamed and remain only for compatibility.

Returns an Array of KEGG/PATHWAY ID in CLASS field.

references ()

Source

   # File lib/bio/db/kegg/orthology.rb
60 def references; super; end

REFERENCE – Returns contents of the REFERENCE records as an Array of Bio::Reference objects.

Returns: an Array containing Bio::Reference objects

Calls superclass method Bio::KEGG::Common::References#references

class Bio::KEGG::ORTHOLOGY

Description¶ ↑

References¶ ↑

`References`¶ ↑