Class: Bio::KEGG::ORTHOLOGY

Inherits:
Bio::KEGGDB show all
Includes:
Common::DblinksAsHash, Common::GenesAsHash, Common::ModulesAsHash, Common::PathwaysAsHash, Common::References
Defined in:
lib/bio/db/kegg/orthology.rb

Overview

Description

KO (KEGG Orthology) entry parser.

References

Constant Summary collapse

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

Instance Method Summary collapse

Methods inherited from DB

#exists?, #fetch, #get, open, #tags

Constructor Details

#initialize(entry) ⇒ ORTHOLOGY

Reads a flat file format entry of the KO database.



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# File 'lib/bio/db/kegg/orthology.rb', line 63

def initialize(entry)
  super(entry, TAGSIZE)
end

Instance Method Details

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



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# File 'lib/bio/db/kegg/orthology.rb', line 33

def dblinks_as_hash; super; end

#dblinks_as_strings ⇒ Object

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



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# File 'lib/bio/db/kegg/orthology.rb', line 121

def dblinks_as_strings
  lines_fetch('DBLINKS')
end

#definition ⇒ Object

Returns DEFINITION field of the entry.



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# File 'lib/bio/db/kegg/orthology.rb', line 83

def definition
  field_fetch('DEFINITION')
end

#entry_id ⇒ Object

Returns ID of the entry.



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# File 'lib/bio/db/kegg/orthology.rb', line 68

def entry_id
  field_fetch('ENTRY')[/\S+/]
end

#genes_as_hash ⇒ Object Also known as: genes

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



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# File 'lib/bio/db/kegg/orthology.rb', line 38

def genes_as_hash; super; end

#genes_as_strings ⇒ Object

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



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# File 'lib/bio/db/kegg/orthology.rb', line 126

def genes_as_strings
  lines_fetch('GENES')
end

#keggclass ⇒ Object

Returns CLASS field of the entry.



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# File 'lib/bio/db/kegg/orthology.rb', line 88

def keggclass
  field_fetch('CLASS')
end

#keggclasses ⇒ Object

Returns an Array of biological classes in CLASS field.



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# File 'lib/bio/db/kegg/orthology.rb', line 93

def keggclasses
  keggclass.gsub(/ \[[^\]]+/, '').split(/\] ?/)
end

#modules_as_hash ⇒ Object Also known as: modules

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



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# File 'lib/bio/db/kegg/orthology.rb', line 52

def modules_as_hash; super; end

#modules_as_strings ⇒ Object

Returns MODULE field of the entry.

Returns

Array containing String objects



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# File 'lib/bio/db/kegg/orthology.rb', line 116

def modules_as_strings
  lines_fetch('MODULE')
end

#name ⇒ Object

Returns NAME field of the entry.



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# File 'lib/bio/db/kegg/orthology.rb', line 73

def name
  field_fetch('NAME')
end

#names ⇒ Object

Returns an Array of names in NAME field.



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# File 'lib/bio/db/kegg/orthology.rb', line 78

def names
  name.split(', ')
end

#pathways_as_hash ⇒ Object Also known as: pathways

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



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# File 'lib/bio/db/kegg/orthology.rb', line 43

def pathways_as_hash; super; end

#pathways_as_strings ⇒ Object

Pathways described in the PATHWAY field.

Returns

Array containing String



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# File 'lib/bio/db/kegg/orthology.rb', line 100

def pathways_as_strings
  lines_fetch('PATHWAY')
end

#pathways_in_keggclass ⇒ Object

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.



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# File 'lib/bio/db/kegg/orthology.rb', line 109

def pathways_in_keggclass
  keggclass.scan(/\[PATH:(.*?)\]/).flatten
end

#references ⇒ Object

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

Returns

an Array containing Bio::Reference objects



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# File 'lib/bio/db/kegg/orthology.rb', line 60

def references; super; end