Method: Bio::EMBL#os

Defined in:
lib/bio/db/embl/embl.rb

#os(num = nil) ⇒ Object

returns contents in the OS line.

  • Bio::EMBL#os -> Array of <OS Hash>

where <OS Hash> is:

[{'name'=>'Human', 'os'=>'Homo sapiens'}, 
 {'name'=>'Rat', 'os'=>'Rattus norveticus'}]

–

  • Bio::EMBL#os(0) => “Homo sapiens (Human)”

++

OS Line; organism species (>=1)

OS   Trifolium repens (white clover)

Typically, OS line shows “Genus species (name)” style:

OS   Genus species (name)

Other examples:

OS   uncultured bacterium
OS   xxxxxx metagenome
OS   Cloning vector xxxxxxxx

Complicated examples:

OS   Poeciliopsis gracilis (Poeciliopsis gracilis (Heckel, 1848))
OS   Etmopterus sp. B Last & Stevens, 1994 (bristled lanternshark)
OS   Galaxias sp. D (Allibone et al., 1996) (Pool Burn galaxias)
OS   Sicydiinae sp. 'Keith et al., 2010'
OS   Acanthopagrus sp. 'Jean & Lee, 2008'
OS   Gaussia princeps (T. Scott, 1894)
OS   Rana sp. 8 Hillis & Wilcox, 2005
OS   Contracaecum rudolphii C D'Amelio et al., 2007
OS   Partula sp. 'Mt. Marau, Tahiti'
OS   Leptocephalus sp. 'type II larva' (Smith, 1989)
OS   Tayloria grandis (D.G.Long) Goffinet & A.J.Shaw, 2002
OS   Non-A, non-B hepatitis virus
OS   Canidae (dog, coyote, wolf, fox)
OS   Salmonella enterica subsp. enterica serovar 4,[5],12:i:-
OS   Yersinia enterocolitica (type O:5,27)
OS   Influenza A virus (A/green-winged teal/OH/72/99(H6N1,4))
OS   Influenza A virus (A/Beijing/352/1989,(highgrowth reassortant NIB26)(H3N2))
OS   Recombinant Hepatitis C virus H77(5'UTR-NS2)/JFH1_V787A,Q1247L



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# File 'lib/bio/db/embl/embl.rb', line 266

def os(num = nil)
  unless @data['OS']
    os = Array.new
    tmp = fetch('OS')
    if /([A-Z][a-z]* *[\w \:\'\+\-]+\w) *\(([\w ]+)\)\s*\z/ =~ tmp
      org = $1
      name = $2
      os.push({'name' => name, 'os' => org})
    else
      os.push({'name' => nil, 'os' => tmp})
    end
    @data['OS'] = os
  end
  if num
    # EX. "Trifolium repens (white clover)"
    "#{@data['OS'][num]['os']} {#data['OS'][num]['name']"
  end
  @data['OS']
end