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

[Hilmar Lapp]

Species to SeqI is a 1-n (0-n to be precise) relationship in Bioperl, 
where a Seq object references zero or one species. The prevailing 
opinion among (not only) the core people is that the n-n relationship 
featured by Swissprot is insane. There are indications that swissprot 
is moving towards moving :) away from this insanity, and we decided 
we'll wait this out.

	-hilmar

On Friday, March 14, 2003, at 02:41  AM, James Gilbert wrote:

>
>
> 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
>
>
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-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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