Module: Entrez

Defined in:
lib/rbbt/sources/entrez.rb

Defined Under Namespace

Classes: Gene

Class Method Summary collapse

Class Method Details

.entrez2name(taxs, options = {}) ⇒ Object 



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# File 'lib/rbbt/sources/entrez.rb', line 37

def self.entrez2name(taxs, options = {})
  options = Misc.add_defaults options, :key_field => 1, :fields => [2], :persist => true, :merge => true

  taxs = [taxs] unless Array === taxs
  options.merge! :grep => taxs.collect{|t| "^" + t.to_s}, :fixed_grep => false

  tsv = Rbbt.share.databases.entrez.gene_info.tsv :flat, options
  tsv.key_field = "Entrez Gene ID"
  tsv.fields    = ["Associated Gene Name"]
  tsv
end

.entrez2native(taxs, options = {}) ⇒ Object 



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# File 'lib/rbbt/sources/entrez.rb', line 25

def self.entrez2native(taxs, options = {})
  options = Misc.add_defaults options, :key_field => 1, :fields => [5], :persist => true, :merge => true

  taxs = [taxs] unless Array === taxs
  options.merge! :grep => taxs.collect{|t| "^" + t.to_s}, :fixed_grep => false

  tsv = Rbbt.share.databases.entrez.gene_info.tsv :flat, options
  tsv.key_field = "Entrez Gene ID"
  tsv.fields    = ["Native ID"]
  tsv
end

.entrez2pubmed(taxs) ⇒ Object 



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# File 'lib/rbbt/sources/entrez.rb', line 50

def self.entrez2pubmed(taxs)
  options = {:key_field => 1, :fields => [2], :persist => true, :merge => true}

  taxs = [taxs] unless taxs.is_a?(Array)
  options.merge! :grep => taxs.collect{|t| "^" + t.to_s}, :fixed_grep => false

  Rbbt.share.databases.entrez.gene2pubmed.tsv :flat, options
end