Contents

require 'rbbt-util'
require 'rbbt/sources/biomart'
require 'rbbt/sources/entrez'

def tsv_file(url, native, extra, options = {})
  options = Misc.add_defaults options, :persistence => false, :keep_empty => true

  case
  when Array === native
    options = Misc.add_defaults options, :native => native.last 
    key_field = native.first
  when (String === native or Integer === native)
    options = Misc.add_defaults options, :native => native
    key_field = nil
  else
    key_field = nil
  end

  case
  when (Array === extra and Array === extra.first)
    options = Misc.add_defaults options, :extra => extra.collect{|e| e.last}
    fields = extra.collect{|e| e.first}
  when (Array === extra and not Array === extra.first)
    options = Misc.add_defaults options, :extra => extra
    fields = (1..extra.length).to_a.collect{|i| "Field#{i}"}
  else
    fields = nil
  end

  tsv = TSV.new(Open.open(url), options)
  tsv.key_field ||= key_field
  tsv.fields ||= fields
  tsv
end

def merge_entrez(data, taxs, native, fix = nil, select = nil)
  entrez =  Entrez.entrez2native(taxs, :fix => fix, :select => select)
  entrez.fields = [native]
  entrez

  data.smart_merge entrez, native
end

def merge_biomart(lexicon, db, native, other, match = nil)
  match ||= native.first
  lexicon.smart_merge BioMart.tsv(db, native, other), match
end

Version data entries

3 entries across 3 versions & 1 rubygems

Version	Path
rbbt-sources-0.2.2	share/install/lib/helpers.rb
rbbt-sources-0.2.1	share/install/lib/helpers.rb
rbbt-sources-0.2.0	share/install/lib/helpers.rb