[Bioperl-l] Gaps in sequences

[Holland, Richard]

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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