[Bioperl-l] bioperl can't read Y08502

Ewan Birney birney@ebi.ac.uk
Mon, 14 May 2001 17:15:43 +0100 (BST)


On Mon, 14 May 2001, Kris Boulez wrote:

> Bioperl can't process an EMBL formatted file containing the entry
> MIATGENB from EMBL (accession number Y08502). One gets errors like
> 
>   -------------------- WARNING ---------------------
>   MSG: unable to parse location successfully out of
>   complement(Y08501:146990..147048), ignoring feature (seqid=MIATGENB)
>   ---------------------------------------------------
>   -------------------- WARNING ---------------------
>   MSG: unable to parse location successfully out of
>   complement(Y08501:143219..143477), ignoring feature (seqid=MIATGENB)
>   ---------------------------------------------------
>   Can't call method "location" on an undefined value at
>   /usr/local/lib/perl5/site_perl/5.005/Bio/SeqIO/FTHelper.pm line 136,
>   <GEN0> chunk 506.
> 
> Removing all features which refer to another entry
> ("complement(Y08501:146990..147048)") solves the problem and makes
> bioperl happy.

Have you tried main trunk. I believe this has been fixed there.

> 
> Kris,
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
> 

-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
-----------------------------------------------------------------