Class Bio::KEGG::MODULE
In: lib/bio/db/kegg/module.rb
Parent: KEGGDB

Methods

Included Modules

Common::StringsAsHash

Constants

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

Public Class methods

Creates a new Bio::KEGG::MODULE object.


Arguments:

  • (required) entry: (String) single entry as a string
Returns:Bio::KEGG::MODULE object

[Source]

    # File lib/bio/db/kegg/module.rb, line 41
41:   def initialize(entry)
42:     super(entry, TAGSIZE)
43:   end

Public Instance methods

compounds()

Alias for compounds_as_hash

Compounds described in the COMPOUND lines.


Returns:Hash of compound ID and its definition

[Source]

     # File lib/bio/db/kegg/module.rb, line 147
147:   def compounds_as_hash
148:     unless @compounds_as_hash
149:       @compounds_as_hash = strings_as_hash(compounds_as_strings)
150:     end
151:     @compounds_as_hash
152:   end

Compounds described in the COMPOUND lines.


Returns:Array containing String

[Source]

     # File lib/bio/db/kegg/module.rb, line 140
140:   def compounds_as_strings
141:     lines_fetch('COMPOUND')
142:   end

Definition of the module, described in the DEFINITION line.


Returns:String

[Source]

    # File lib/bio/db/kegg/module.rb, line 62
62:   def definition
63:     field_fetch('DEFINITION')
64:   end

Return the ID, described in the ENTRY line.


Returns:String

[Source]

    # File lib/bio/db/kegg/module.rb, line 48
48:   def entry_id
49:     field_fetch('ENTRY')[/\S+/]
50:   end

Name of the KEGG class, described in the CLASS line.


Returns:String

[Source]

    # File lib/bio/db/kegg/module.rb, line 69
69:   def keggclass
70:     field_fetch('CLASS')
71:   end

Name of the module, described in the NAME line.


Returns:String

[Source]

    # File lib/bio/db/kegg/module.rb, line 55
55:   def name
56:     field_fetch('NAME')
57:   end
orthologs()

Alias for orthologs_as_hash

All KO IDs in the ORTHOLOGY lines.


Returns:Array of orthology IDs

[Source]

     # File lib/bio/db/kegg/module.rb, line 113
113:   def orthologs_as_array
114:     orthologs_as_hash.keys.map{|x| x.split(/\+|\-|,/)}.flatten.sort.uniq
115:   end

Orthologs described in the ORTHOLOGY lines.


Returns:Hash of orthology ID and its definition

[Source]

     # File lib/bio/db/kegg/module.rb, line 102
102:   def orthologs_as_hash
103:     unless @orthologs_as_hash
104:       @orthologs_as_hash = strings_as_hash(orthologs_as_strings)
105:     end
106:     @orthologs_as_hash
107:   end

Orthologs described in the ORTHOLOGY lines.


Returns:Array containing String

[Source]

    # File lib/bio/db/kegg/module.rb, line 95
95:   def orthologs_as_strings
96:     lines_fetch('ORTHOLOGY')
97:   end
pathways()

Alias for pathways_as_hash

Pathways described in the PATHWAY lines.


Returns:Hash of pathway ID and its definition

[Source]

    # File lib/bio/db/kegg/module.rb, line 83
83:   def pathways_as_hash
84:     unless @pathways_as_hash
85:       @pathways_as_hash = strings_as_hash(pathways_as_strings)
86:     end
87:     @pathways_as_hash
88:   end

Pathways described in the PATHWAY lines.


Returns:Array containing String

[Source]

    # File lib/bio/db/kegg/module.rb, line 76
76:   def pathways_as_strings
77:     lines_fetch('PATHWAY')
78:   end
reactions()

Alias for reactions_as_hash

Reactions described in the REACTION lines.


Returns:Hash of reaction ID and its definition

[Source]

     # File lib/bio/db/kegg/module.rb, line 128
128:   def reactions_as_hash
129:     unless @reactions_as_hash
130:       @reactions_as_hash = strings_as_hash(reactions_as_strings)
131:     end
132:     @reactions_as_hash
133:   end

Reactions described in the REACTION lines.


Returns:Array containing String

[Source]

     # File lib/bio/db/kegg/module.rb, line 121
121:   def reactions_as_strings
122:     lines_fetch('REACTION')
123:   end

[Validate]