Class: Bio::KEGG::ORTHOLOGY

Inherits:

Bio::KEGGDB

• Object
• DB
• NCBIDB
• Bio::KEGGDB
• Bio::KEGG::ORTHOLOGY

show all

Includes:

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

Defined in:

lib/bio/db/kegg/orthology.rb

Overview

Constant Summary

DELIMITER =

RS = "\n///\n"

TAGSIZE =

12

Instance Method Summary (collapse)

• - (Object) dblinks_as_hash (also: #dblinks)
• - (Object) dblinks_as_strings

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

• - (Object) definition

  Returns DEFINITION field of the entry.

• - (Object) entry_id

  Returns ID of the entry.

• - (Object) genes_as_hash (also: #genes)
• - (Object) genes_as_strings

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

• - (ORTHOLOGY) initialize(entry) constructor

  Reads a flat file format entry of the KO database.

• - (Object) keggclass

  Returns CLASS field of the entry.

• - (Object) keggclasses

  Returns an Array of biological classes in CLASS field.

• - (Object) modules_as_hash (also: #modules)
• - (Object) modules_as_strings

  Returns MODULE field of the entry.

• - (Object) name

  Returns NAME field of the entry.

• - (Object) names

  Returns an Array of names in NAME field.

• - (Object) pathways_as_hash (also: #pathways)
• - (Object) pathways_as_strings

  Pathways described in the PATHWAY field.

• - (Object) pathways_in_keggclass

  OBSOLETE Do not use this method.

• - (Object) references

Methods inherited from DB

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

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

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

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

def dblinks_as_hash; super; end

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

def dblinks_as_strings
  lines_fetch('DBLINKS')
end

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

def definition
  field_fetch('DEFINITION')
end

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

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

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

def genes_as_hash; super; end

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

def genes_as_strings
  lines_fetch('GENES')
end

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

def keggclass
  field_fetch('CLASS')
end

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

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

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

def modules_as_hash; super; end

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

def modules_as_strings
  lines_fetch('MODULE')
end

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

def name
  field_fetch('NAME')
end

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

def names
  name.split(', ')
end

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

def pathways_as_hash; super; end

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

def pathways_as_strings
  lines_fetch('PATHWAY')
end

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

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

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

def references; super; end