Class Bio::KEGG::ORTHOLOGY
In: lib/bio/db/kegg/orthology.rb
Parent: KEGGDB

Methods

Included Modules

Common::DblinksAsHash Common::GenesAsHash Common::PathwaysAsHash Common::ModulesAsHash Common::References

Constants

DELIMITER = RS = "\n///\n"
TAGSIZE = 12

Public Class methods

Reads a flat file format entry of the KO database.

[Source]

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

Public Instance methods

dblinks()

Alias for dblinks_as_hash

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

[Source]

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

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

[Source]

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

Returns DEFINITION field of the entry.

[Source]

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

Returns ID of the entry.

[Source]

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

Alias for genes_as_hash

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

[Source]

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

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

[Source]

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

Returns CLASS field of the entry.

[Source]

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

Returns an Array of biological classes in CLASS field.

[Source]

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

Alias for modules_as_hash

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

[Source]

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

Returns MODULE field of the entry.


Returns:Array containing String objects

[Source]

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

Returns NAME field of the entry.

[Source]

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

Returns an Array of names in NAME field.

[Source]

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

Alias for pathways_as_hash

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

[Source]

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

Pathways described in the PATHWAY field.


Returns:Array containing String

[Source]

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

[Source]

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

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


Returns:an Array containing Bio::Reference objects

[Source]

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

[Validate]