Module: ArrayExpress

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

Class Method Summary collapse

Class Method Details

.tpm(code, organism = Organism.default_code("Hsa")) ⇒ Object 



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# File 'lib/rbbt/sources/array_express.rb', line 3

def self.tpm(code, organism = Organism.default_code("Hsa"))
  url = "https://www.ebi.ac.uk/gxa/experiments-content/#{code}/resources/ExperimentDownloadSupplier.RnaSeqBaseline/tpms.tsv"
  io = TSV.traverse Open.open(url), :type => :line, :into => :stream do |line|
    next if line =~ /^#/
    parts = line.split("\t")
    line = parts[0] << "\t" << parts[2..-1] * "\t"
    line = "#" + line if line =~ /Gene ID/
    line
  end
  tsv = TSV.open(io, :type => :list, :cast => :to_f)
  tsv.key_field = "Ensembl Gene ID"
  tsv.namespace = organism
  tsv
end