class Bio::KEGG::PATHWAY

Description¶ ↑

Bio::KEGG::PATHWAY is a parser class for the KEGG PATHWAY database entry.

`References`¶ ↑

Constants

DELIMITER
TAGSIZE

Public Class Methods

Source

   # File lib/bio/db/kegg/pathway.rb
76 def initialize(entry)
77   super(entry, TAGSIZE)
78 end

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

Arguments:

(required) entry: (String) single entry as a string

Returns: Bio::KEGG::PATHWAY object

Calls superclass method Bio::NCBIDB::new

Public Instance Methods

compounds ()

Alias for: compounds_as_hash

compounds_as_hash ()

Source

    # File lib/bio/db/kegg/pathway.rb
205 def compounds_as_hash
206   unless (defined? @compounds_as_hash) && @compounds_as_hash
207     @compounds_as_hash = strings_as_hash(compounds_as_strings)
208   end
209   @compounds_as_hash
210 end

Compounds described in the COMPOUND lines.

Returns: Hash of compound ID and its definition

Also aliased as: compounds

compounds_as_strings ()

Source

    # File lib/bio/db/kegg/pathway.rb
198 def compounds_as_strings
199   lines_fetch('COMPOUND')
200 end

Compounds described in the COMPOUND lines.

Returns: Array containing String

dblinks ()

Alias for: dblinks_as_hash

dblinks_as_hash ()

Source

   # File lib/bio/db/kegg/pathway.rb
32 def dblinks_as_hash; super; end

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

Calls superclass method Bio::KEGG::Common::DblinksAsHash#dblinks_as_hash

Also aliased as: dblinks

dblinks_as_strings ()

Source

    # File lib/bio/db/kegg/pathway.rb
133 def dblinks_as_strings
134   lines_fetch('DBLINKS')
135 end

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

Returns: Array containing String

definition ()

Alias for: description

description ()

Source

   # File lib/bio/db/kegg/pathway.rb
97 def description
98   field_fetch('DESCRIPTION')
99 end

Description of the pathway, described in the DESCRIPTION line.

Returns: String

Also aliased as: definition

diseases ()

Alias for: diseases_as_hash

diseases_as_hash ()

Source

   # File lib/bio/db/kegg/pathway.rb
47 def diseases_as_hash; super; end

Returns a Hash of the disease ID and its definition

Calls superclass method Bio::KEGG::Common::DiseasesAsHash#diseases_as_hash

Also aliased as: diseases

diseases_as_strings ()

Source

    # File lib/bio/db/kegg/pathway.rb
126 def diseases_as_strings
127   lines_fetch('DISEASE')
128 end

Disease described in the DISEASE lines.

Returns: Array containing String

entry_id ()

Source

   # File lib/bio/db/kegg/pathway.rb
83 def entry_id
84   field_fetch('ENTRY')[/\S+/]
85 end

Return the ID of the pathway, described in the ENTRY line.

Returns: String

enzymes ()

Alias for: enzymes_as_strings

enzymes_as_strings ()

Source

    # File lib/bio/db/kegg/pathway.rb
172 def enzymes_as_strings
173   lines_fetch('ENZYME')
174 end

Enzymes described in the ENZYME lines.

Returns: Array containing String

Also aliased as: enzymes

genes ()

Alias for: genes_as_hash

genes_as_hash ()

Source

    # File lib/bio/db/kegg/pathway.rb
161 def genes_as_hash
162   unless (defined? @genes_as_hash) && @genes_as_hash
163     @genes_as_hash = strings_as_hash(genes_as_strings)
164   end
165   @genes_as_hash
166 end

Genes described in the GENE lines.

Returns: Hash of gene ID and its definition

Also aliased as: genes

genes_as_strings ()

Source

    # File lib/bio/db/kegg/pathway.rb
154 def genes_as_strings
155   lines_fetch('GENE')
156 end

Genes described in the GENE lines.

Returns: Array containing String

keggclass ()

Source

    # File lib/bio/db/kegg/pathway.rb
105 def keggclass
106   field_fetch('CLASS')
107 end

Return the name of the KEGG class, described in the CLASS line.

Returns: String

ko_pathway ()

Source

    # File lib/bio/db/kegg/pathway.rb
240 def ko_pathway
241   field_fetch('KO_PATHWAY')
242 end

KO pathway described in the KO_PATHWAY line.

Returns: String

modules ()

Alias for: modules_as_hash

modules_as_hash ()

Source

   # File lib/bio/db/kegg/pathway.rb
63 def modules_as_hash; super; end

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

Calls superclass method Bio::KEGG::Common::ModulesAsHash#modules_as_hash

Also aliased as: modules

modules_as_strings ()

Source

    # File lib/bio/db/kegg/pathway.rb
119 def modules_as_strings
120   lines_fetch('MODULE')
121 end

Returns MODULE field of the entry.

Returns: Array containing String objects

name ()

Source

   # File lib/bio/db/kegg/pathway.rb
90 def name
91   field_fetch('NAME')
92 end

Name of the pathway, described in the NAME line.

Returns: String

organism ()

Source

    # File lib/bio/db/kegg/pathway.rb
147 def organism
148   field_fetch('ORGANISM')
149 end

Organism described in the ORGANISM line.

Returns: String

orthologs ()

Alias for: orthologs_as_hash

orthologs_as_hash ()

Source

   # File lib/bio/db/kegg/pathway.rb
42 def orthologs_as_hash; super; end

Returns a Hash of the orthology ID and definition in ORTHOLOGY field.

Calls superclass method Bio::KEGG::Common::OrthologsAsHash#orthologs_as_hash

Also aliased as: orthologs

orthologs_as_strings ()

Source

    # File lib/bio/db/kegg/pathway.rb
140 def orthologs_as_strings
141   lines_fetch('ORTHOLOGY')
142 end

Orthologs described in the ORTHOLOGY lines.

Returns: Array containing String

pathways ()

Alias for: pathways_as_hash

pathways_as_hash ()

Source

   # File lib/bio/db/kegg/pathway.rb
37 def pathways_as_hash; super; end

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

Calls superclass method Bio::KEGG::Common::PathwaysAsHash#pathways_as_hash

Also aliased as: pathways

pathways_as_strings ()

Source

    # File lib/bio/db/kegg/pathway.rb
112 def pathways_as_strings
113   lines_fetch('PATHWAY_MAP')
114 end

Pathways described in the PATHWAY_MAP lines.

Returns: Array containing String

reactions ()

Alias for: reactions_as_hash

reactions_as_hash ()

Source

    # File lib/bio/db/kegg/pathway.rb
187 def reactions_as_hash
188   unless (defined? @reactions_as_hash) && @reactions_as_hash
189     @reactions_as_hash = strings_as_hash(reactions_as_strings)
190   end
191   @reactions_as_hash
192 end

Reactions described in the REACTION lines.

Returns: Hash of reaction ID and its definition

Also aliased as: reactions

reactions_as_strings ()

Source

    # File lib/bio/db/kegg/pathway.rb
180 def reactions_as_strings
181   lines_fetch('REACTION')
182 end

Reactions described in the REACTION lines.

Returns: Array containing String

references ()

Source

   # File lib/bio/db/kegg/pathway.rb
55 def references; super; end

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

Returns: an Array containing Bio::Reference objects

Calls superclass method Bio::KEGG::Common::References#references

rel_pathways ()

Alias for: rel_pathways_as_hash

rel_pathways_as_hash ()

Source

    # File lib/bio/db/kegg/pathway.rb
224 def rel_pathways_as_hash
225   unless defined? @rel_pathways_as_hash then
226     hash = {}
227     rel_pathways_as_strings.each do |line|
228       entry_id, name = line.split(/\s+/, 2)
229       hash[entry_id] = name
230     end
231     @rel_pathways_as_hash = hash
232   end
233   @rel_pathways_as_hash
234 end

Returns REL_PATHWAY field as a Hash. Each key of the hash is Pathway ID, and each value is the name of the pathway.

Returns: Hash

Also aliased as: rel_pathways

rel_pathways_as_strings ()

Source

    # File lib/bio/db/kegg/pathway.rb
216 def rel_pathways_as_strings
217   lines_fetch('REL_PATHWAY')
218 end

Returns REL_PATHWAY field of the entry.

Returns: Array containing String objects

class Bio::KEGG::PATHWAY

Description¶ ↑

References¶ ↑

`References`¶ ↑