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

[Heikki Lehvaslaiho]

At the moment the parser takes the last OS field. I think we should keep
the bug open  until it is fixed to take in the first one which matches
the OC line.

http://bugzilla.bioperl.org/show_bug.cgi?id=1410

	-Heikki



On Fri, 2003-03-14 at 19:07, Hilmar Lapp wrote:
> 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
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> >
-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki at ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________