[Bioperl-l] One more odd little parsing problem for your list

[Heikki Lehvaslaiho]

Michael,

Rather than we trying to fix this in bioperl, could you report this to
NCBI helpdesk. There really are some rules even if RefSeq entries are
not officially and strictly following GenBank format. This case has to
be a bug.

	-Heikki


 On Sun, 2003-06-01 at 08:32, Hilmar Lapp wrote:
> Ouch, a space in the locus identifier. Why do they do this to us.
> 
> I'm afraid I have to kludge this. We can't afford the genbank parser 
> dying on Genbank's random pranks. Isn't this fun.
> 
> 	-hilmar
> 
> On Saturday, May 31, 2003, at 12:00  PM, Michael Muratet wrote:
> 
> > Greetings
> >
> > I was parsing CDS features in Refseq human (hs.gbff.gz) when it died on
> > PSMAL/GCP III (NM_153696). The CDS was 527..1855. The error was from
> > Bio::PrimarySeq::subseq 'You have to start positive....sequence
> > [527:1855] Total III'. The parser in SeqIO is picking up the length 
> > from
> > the LOCUS line (as I recall) and for this record it sees 'III' and not
> > '1992' bp. It seems a lot to ask Bioperl to figure out every possible
> > configuration, maybe Genbank needs to have rules about whitespace in
> > gene names?
> >
> > Cheers
> >
> > Mike
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
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      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
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______________________________________________________________________
      
      Heikki Lehväslaiho     -     heikki/at/bioperl.org
______________________________________________________________________