class Bio::KEGG::MODULE
Description¶ ↑
Bio::KEGG::MODULE is a parser class for the KEGG MODULE database entry.
References¶ ↑
Constants
- DELIMITER
- TAGSIZE
Public Class Methods
new(entry)
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Creates a new Bio::KEGG::MODULE object.
Arguments:
-
(required) entry: (String) single entry as a string
- Returns
-
Bio::KEGG::MODULE object
Calls superclass method
Bio::NCBIDB.new
# File lib/bio/db/kegg/module.rb, line 41 def initialize(entry) super(entry, TAGSIZE) end
Public Instance Methods
compounds_as_hash()
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Compounds described in the COMPOUND lines.
- Returns
-
Hash of compound ID and its definition
# File lib/bio/db/kegg/module.rb, line 147 def compounds_as_hash unless @compounds_as_hash @compounds_as_hash = strings_as_hash(compounds_as_strings) end @compounds_as_hash end
Also aliased as: compounds
compounds_as_strings()
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definition()
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Definition of the module, described in the DEFINITION line.
- Returns
# File lib/bio/db/kegg/module.rb, line 62 def definition field_fetch('DEFINITION') end
entry_id()
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Return the ID, described in the ENTRY line.
- Returns
# File lib/bio/db/kegg/module.rb, line 48 def entry_id field_fetch('ENTRY')[/\S+/] end
keggclass()
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name()
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Name of the module, described in the NAME line.
- Returns
# File lib/bio/db/kegg/module.rb, line 55 def name field_fetch('NAME') end
orthologs_as_array()
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All KO IDs in the ORTHOLOGY lines.
- Returns
-
Array of orthology IDs
# File lib/bio/db/kegg/module.rb, line 113 def orthologs_as_array orthologs_as_hash.keys.map{|x| x.split(/\+|\-|,/)}.flatten.sort.uniq end
orthologs_as_hash()
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Orthologs described in the ORTHOLOGY lines.
- Returns
-
Hash of orthology ID and its definition
# File lib/bio/db/kegg/module.rb, line 102 def orthologs_as_hash unless @orthologs_as_hash @orthologs_as_hash = strings_as_hash(orthologs_as_strings) end @orthologs_as_hash end
Also aliased as: orthologs
orthologs_as_strings()
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pathways_as_hash()
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Pathways described in the PATHWAY lines.
- Returns
-
Hash of pathway ID and its definition
# File lib/bio/db/kegg/module.rb, line 83 def pathways_as_hash unless @pathways_as_hash @pathways_as_hash = strings_as_hash(pathways_as_strings) end @pathways_as_hash end
Also aliased as: pathways
pathways_as_strings()
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reactions_as_hash()
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Reactions described in the REACTION lines.
- Returns
-
Hash of reaction ID and its definition
# File lib/bio/db/kegg/module.rb, line 128 def reactions_as_hash unless @reactions_as_hash @reactions_as_hash = strings_as_hash(reactions_as_strings) end @reactions_as_hash end
Also aliased as: reactions