Module: InterPro

Extended by:
Resource
Defined in:
lib/rbbt/sources/pfam.rb,
lib/rbbt/sources/InterPro.rb

Class Method Summary collapse

Class Method Details

.domain_index ⇒ Object 



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# File 'lib/rbbt/sources/InterPro.rb', line 44

def self.domain_index
  @@domain_index ||= InterPro.protein_domains.tsv(:persist => true, :unnamed => true, :key_field => "UniProt/SwissProt Accession", :fields => ["InterPro ID"], :merge => true)
end

.domain_position_index ⇒ Object 



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# File 'lib/rbbt/sources/InterPro.rb', line 48

def self.domain_position_index
  @@domain_position_index ||= InterPro.protein_domains.tsv(:persist => true, :unnamed => true, :key_field => "UniProt/SwissProt Accession", :fields => ["InterPro ID", "Domain Start AA", "Domain End AA"], :type => :double, :merge => true)
end

.ens2uniprot(organism) ⇒ Object 



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# File 'lib/rbbt/sources/InterPro.rb', line 52

def self.ens2uniprot(organism)
  @@ens2uniprot_index ||= {}
  @@ens2uniprot_index[organism] ||= Organism.protein_identifiers(organism).tsv(:persist => true, :unnamed => true, :fields => ["UniProt/SwissProt Accession"], :key_field => "Ensembl Protein ID", :type => :double, :merge => true)
end

.gene_index ⇒ Object 



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# File 'lib/rbbt/sources/InterPro.rb', line 40

def self.gene_index
  @@gene_index ||= InterPro.protein_domains.tsv(:persist => true, :key_field => "InterPro ID", :fields => ["UniProt/SwissProt Accession"], :type => :flat, :merge => true, :unnamed => true)
end

.name_index ⇒ Object 



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# File 'lib/rbbt/sources/InterPro.rb', line 36

def self.name_index
  @@name_index ||= InterPro.domain_names.tsv(:persist => true, :unnamed => true)
end

.pfam_index ⇒ Object 



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# File 'lib/rbbt/sources/pfam.rb', line 52

def self.pfam_index
  @@pfam_index ||= InterPro.pfam_equivalences.tsv(:persist => true, :key_field => "InterPro ID", :fields => ["Pfam Domain"])
end