[Bioperl-l] error retrieving AF001282 from genbank

[Jason Stajich]

what version of bioperl are you using?
what does 
% perldoc -m Bio::SeqIO::genbank | grep Id 
return?

This was fixed in the soon-to-be-released bioperl 0.7.1 and on bioperl
main-trunk a while ago.

Bioperl: We need to start a FAQ...

-jason

On Mon, 18 Jun 2001, Hao Chen wrote:

> 
> 
> Hello,
> 
> I am not able to get the seq of AF001282 from
> genbank using the following code:
> 
> use Bio::DB::GenBank;
> $gb = new Bio::DB::Genbank();
> $seq = $gb->get_Seq_by_acc ("AF001282");
> 
> The following error message was reported.
> -------------------- WARNING ---------------------
> MSG: unable to parse location successfully out of AF001278.1:675..701, 
> ignoring
> feature (seqid=RNHGPRT4)
> ---------------------------------------------------
> -------------------- WARNING ---------------------
> MSG: unable to parse location successfully out of AF009655.1:275..381, 
> ignoring
> feature (seqid=RNHGPRT4)
> ---------------------------------------------------
> -------------------- WARNING ---------------------
> MSG: unable to parse location successfully out of AF009656.1:126..309, 
> ignoring
> feature (seqid=RNHGPRT4)
> ---------------------------------------------------
> -------------------- WARNING ---------------------
> MSG: unable to parse location successfully out of AF001280.1:215..232, 
> ignoring
> feature (seqid=RNHGPRT4)
> ---------------------------------------------------
> -------------------- WARNING ---------------------
> MSG: unable to parse location successfully out of AF001281.1:191..273, 
> ignoring
> feature (seqid=RNHGPRT4)
> ---------------------------------------------------
> -------------------- WARNING ---------------------
> MSG: unable to parse location successfully out of AF001282.1:378..424, 
> ignoring
> feature (seqid=RNHGPRT4)
> ---------------------------------------------------
> -------------------- WARNING ---------------------
> MSG: unable to parse location successfully out of AF001282.1:595..671, 
> ignoring
> feature (seqid=RNHGPRT4)
> ---------------------------------------------------
> -------------------- WARNING ---------------------
> MSG: unable to parse location successfully out of AF001282.1:1349..1396, 
> ignoring feature (seqid=RNHGPRT4)
> ---------------------------------------------------
> Can't call method "location" on an undefined value at 
> /usr/lib/perl5/site_perl/5.6.0/Bio/SeqIO/FTHelper.pm line 136.
> 
> 
> 
> Is there anyway arround this? Many thanks in
> advance.
> 
> Hao Chen
> University of Tennessee at Memphis
> 
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> 

Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/