Module: KEGG
- Extended by:
- Resource
- Defined in:
- lib/rbbt/sources/kegg.rb
Class Method Summary collapse
- .description(id) ⇒ Object
- .descriptions ⇒ Object
- .id2name(id) ⇒ Object
- .index2ens ⇒ Object
- .index2genes ⇒ Object
- .index2kegg ⇒ Object
- .name2id(name) ⇒ Object
- .names ⇒ Object
Class Method Details
.description(id) ⇒ Object
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# File 'lib/rbbt/sources/kegg.rb', line 42 def self.description(id) descriptions[id] end |
.descriptions ⇒ Object
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# File 'lib/rbbt/sources/kegg.rb', line 16 def self.descriptions @@descriptions ||= KEGG.pathways.tsv(:fields => ["Pathway Description"], :persist => true, :type => :single, :unnamed => true) end |
.id2name(id) ⇒ Object
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# File 'lib/rbbt/sources/kegg.rb', line 33 def self.id2name(id) names[id] end |
.index2ens ⇒ Object
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# File 'lib/rbbt/sources/kegg.rb', line 25 def self.index2ens @@index2ens ||= KEGG.identifiers.index(:persist => true) end |
.index2genes ⇒ Object
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# File 'lib/rbbt/sources/kegg.rb', line 21 def self.index2genes @@index2genes ||= KEGG.gene_pathway.tsv(:key_field => "KEGG Pathway ID", :fields => ["KEGG Gene ID"], :persist => true, :type => :flat, :merge => true) end |
.index2kegg ⇒ Object
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# File 'lib/rbbt/sources/kegg.rb', line 29 def self.index2kegg @@index2kegg ||= KEGG.identifiers.index(:target => "KEGG Gene ID", :persist => true) end |
.name2id(name) ⇒ Object
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# File 'lib/rbbt/sources/kegg.rb', line 37 def self.name2id(name) names.select{|id,n| n.downcase.index(name.downcase) == 0}.collect{|id,n| id} rescue [] end |
.names ⇒ Object
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# File 'lib/rbbt/sources/kegg.rb', line 12 def self.names @@names ||= KEGG.pathways.tsv :fields => ["Pathway Name"], :persist => true, :type => :single, :unnamed => true end |