Module: InterPro
- Extended by:
- Resource
- Defined in:
- lib/rbbt/sources/pfam.rb,
lib/rbbt/sources/InterPro.rb
Class Method Summary collapse
- .domain_index ⇒ Object
- .domain_position_index ⇒ Object
- .ens2uniprot(organism) ⇒ Object
- .gene_index ⇒ Object
- .name_index ⇒ Object
- .pfam_index ⇒ Object
Class Method Details
.domain_index ⇒ Object
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# File 'lib/rbbt/sources/InterPro.rb', line 42 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 46 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 50 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 38 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 34 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 |