[Bioperl-l] Gaps in sequences

[Jason Stajich]

http://bugzilla.open-bio.org/show_bug.cgi?id=1319

No one has fixed this yet AFAIK.

-jason

On Tue, 6 Jan 2004, Holland, Richard wrote:

> Hi,
>
> Some RefSeq sequences I downloaded in GenBank format from the NCBI have
> interesting location descriptors which cause BioPerl to fail with the
> following error:
>
> -------------------- WARNING ---------------------
> MSG: exception while parsing location line
> [join(AC145223.1:1..25742,gap(646),AC145223.1:26389..31181)] in reading
> EMBL/GenBank/SwissProt, ignoring feature CONTIG (seqid=NT_079570):
> ------------- EXCEPTION  -------------
> MSG: operator "gap" unrecognized by parser
> STACK Bio::Factory::FTLocationFactory::from_string
> /usr/lib/perl-5.8.0/lib/site_perl/5.8.0/Bio/Factory/FTLocationFactory.pm
> :160
> STACK Bio::Factory::FTLocationFactory::from_string
> /usr/lib/perl-5.8.0/lib/site_perl/5.8.0/Bio/Factory/FTLocationFactory.pm
> :157
> STACK (eval)
> /usr/lib/perl-5.8.0/lib/site_perl/5.8.0/Bio/SeqIO/FTHelper.pm:124
> STACK Bio::SeqIO::FTHelper::_generic_seqfeature
> /usr/lib/perl-5.8.0/lib/site_perl/5.8.0/Bio/SeqIO/FTHelper.pm:123
> STACK Bio::SeqIO::genbank::next_seq
> /usr/lib/perl-5.8.0/lib/site_perl/5.8.0/Bio/SeqIO/genbank.pm:421
> STACK toplevel
> /usr/users/oracle/bioperl-db/scripts/biosql/load_seqdatabase.pl:457
>
> --------------------------------------
>
> ---------------------------------------------------
>
> Any ideas anyone? Is this a broken location descriptor, or a broken
> parser? (So far the only ones I have found all occur in
> vertebrate_mammalian3.genomic.gbff)
>
> cheers,
> Richard
>
> ---
> Richard Holland
> Bioinformatics Database Developer
> ITS, Agresearch Invermay x3279
>
>
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu