[Bioperl-l] Gaps in sequences

Holland, Richard Richard.Holland at agresearch.co.nz
Mon Jan 5 16:05:31 EST 2004


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
STACK Bio::Factory::FTLocationFactory::from_string
STACK (eval)
STACK Bio::SeqIO::FTHelper::_generic_seqfeature
STACK Bio::SeqIO::genbank::next_seq
STACK toplevel



Any ideas anyone? Is this a broken location descriptor, or a broken
parser? (So far the only ones I have found all occur in


Richard Holland
Bioinformatics Database Developer
ITS, Agresearch Invermay x3279

Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.

More information about the Bioperl-l mailing list