[BioRuby] Parse string containing GenBenk file?

[Naohisa Goto]

Hi,

If you have a string with single GenBank entry,
you can use Bio::GenBank.new(string).
For example,

  require "bio"
  str = <<__EOF__
LOCUS       A00001                   335 bp    DNA     linear   PAT 11-MAY-2001
DEFINITION  Cauliflower mosaic virus satellite cDNA.
ACCESSION   A00001
VERSION     A00001.1  GI:58418
KEYWORDS    .
SOURCE      Cauliflower mosaic virus
  ORGANISM  Cauliflower mosaic virus
            Viruses; Retro-transcribing viruses; Caulimoviridae; Caulimovirus.
REFERENCE   1  (bases 1 to 335)
  AUTHORS   Baulcombe,D.C., Mayo,M.A., Harrison,B.D. and Bevan,M.W.
  TITLE     Modification of plant viruses or their effects
  JOURNAL   Patent: EP 0242016-A 1 21-OCT-1987;
            AGRICULTURAL GENETICS COMPANY LIMITED
FEATURES             Location/Qualifiers
     source          1..335
                     /organism="Cauliflower mosaic virus"
                     /mol_type="unassigned DNA"
                     /db_xref="taxon:10641"
     misc_feature    1..335
                     /note="satellite DNA"
ORIGIN
        1 gttttgtttg atggagaatt gcgcagaggg gttatatctg cgtgaggatc tgtcactcgg
       61 cggtgtggga tacctccctg ctaaggcggg ttgagtgatg ttccctcgga ctggggaccg
      121 ctggcttgcg agctatgtcc gctactctca gtactacact ctcatttgag cccccgctca
      181 gtttgctagc agaacccggc acatggttcg ccgataccat ggaatttcga aagaaacact
      241 ctgttaggtg gtatgagtca tgacgcacgc agggagaggc taaggcttat gctatgctga
      301 tctccgtgaa tgtctatcat tcctacacag gaccc
//
__EOF__
  
  gb = Bio::GenBank.new(str)
  p gb


If you have a string with multiple entries,
or the string might be other than GenBank (e.g. EMBL.),
using StringIO is better.

  require 'stringio'
  Bio::FlatFile.auto(StringIO.new(string))


Regards,

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org


> Can anyone point me to a method for creating a Bio object from a
> string that contains a Genbank file?
> 
> For example, I have a Genbank file and its contents have been read
> into a single string.  I am unable to use Bio::FlatFile.auto(string)
> to create a Bio object.
> 
> Thanks for the help,
> Karsten
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