[Bioperl-l] Re:Bio::Species Bug/question

[James Gilbert]

Hi Arno,

I guess that the assumption made when writing this
code was that there is only one species per entry.

	James

On Fri, 14 Mar 2003, mailer wrote:

> The following problem occurs with Bio::Species :
>
> In cases of identical sequences for different species there is only one
> Swissprot/Trembl entry with several species lines, as for example for
>
> the Swissprot entry with ID: RAPA_HUMAN;
> The species lines of this entry are:
>
> OS   Homo sapiens (Human),
> OS   Mus musculus (Mouse),
> OS   Rattus norvegicus (Rat), and
> OS   Bos taurus (Bovine).
> OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
> OC   Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo.
>
> I extracted the species information using the following code:
>
> $index = Bio::Index::Swissprot->new('-filename' => './test.dat.idx',
> '-write_flag' => 'WRITE');
> $index->make_index('./test.dat');
> my $indexread = Bio::Index::Swissprot->new('-filename' => './test.dat.idx');
> my $seq = $indexread->get_Seq_by_id('RAPA_HUMAN');
> my $speciesobj = $seq->species();
>
> $species = $speciesobj->binomial();
> $classification = $speciesobj->classification()
>
> Using this code you only retrieve the last species name of the entry
> (Bos
> taurus) and the classification of homo sapiens (which is the only one
> contained
> in the entry).
>
> Is there no possibility to obtain the complete list of species ?
> Thanks for help,
>
> Arno Meiler
>

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
James G.R. Gilbert            The Wellcome Trust Sanger Institute
Fax: +44 (0)1223 494919              Wellcome Trust Genome Campus
Tel: +44 (0)1223 494906              Hinxton, Cambridge, CB10 1SA