Contents

#{{{ FINDER
finder = Finder.new
if ENV['RBBT_FINDER']
  organism = Organism.default_code("Hsa")
  finder.add_instance(KEGG.pathways, :grep => '^hsa\|^#', :fields => ["Pathway Name"], :namespace => organism, :fix => Proc.new{|l| l.sub(/ - Homo sapiens.*/,'')}) if defined? KEGG
  finder.add_instance(Organism.lexicon(organism), :persist => true, :namespace => organism, :grep => Organism.blacklist_genes(organism).list, :invert_grep => true) if defined? Organism

  mutation_hash = {"Genomic Mutation" => /\w+:\d+:[ACTG\-\+]+/}
  finder.add_instance(mutation_hash, :namespace => organism) 

  mi_hash = {"Mutated Isoform" => /ENSP\w+:.+/}
  finder.add_instance(mi_hash, :namespace => organism) 

  prot_hash = {"Ensembl Protein ID" => /ENSP\w+$/}
  finder.add_instance(prot_hash, :namespace => organism) 


  organism_hash = {"organism" => /[A-Z][a-z]{2}(?:\/[a-z]{3}20\d\d)?/}
  finder.add_instance(organism_hash, :namespace => organism) 

  snp_hash = {"SNP" => /^rs\d+$/}
  finder.add_instance(snp_hash, :namespace => organism) 
end
set :finder, finder
Log.debug("Finder started with: #{finder.instances.length} instances")

Version data entries

66 entries across 66 versions & 1 rubygems

Version	Path
rbbt-util-5.21.11	etc/app.d/finder.rb
rbbt-util-5.21.9	etc/app.d/finder.rb
rbbt-util-5.21.8	etc/app.d/finder.rb
rbbt-util-5.21.7	etc/app.d/finder.rb
rbbt-util-5.21.6	etc/app.d/finder.rb
rbbt-util-5.21.5	etc/app.d/finder.rb
rbbt-util-5.21.4	etc/app.d/finder.rb
rbbt-util-5.21.3	etc/app.d/finder.rb
rbbt-util-5.21.2	etc/app.d/finder.rb
rbbt-util-5.21.1	etc/app.d/finder.rb
rbbt-util-5.21.0	etc/app.d/finder.rb
rbbt-util-5.20.26	etc/app.d/finder.rb
rbbt-util-5.20.25	etc/app.d/finder.rb
rbbt-util-5.20.24	etc/app.d/finder.rb
rbbt-util-5.20.23	etc/app.d/finder.rb
rbbt-util-5.20.22	etc/app.d/finder.rb
rbbt-util-5.20.21	etc/app.d/finder.rb
rbbt-util-5.20.20	etc/app.d/finder.rb
rbbt-util-5.20.18	etc/app.d/finder.rb
rbbt-util-5.20.17	etc/app.d/finder.rb