[Bioperl-l] genbank2gff.pl choking on CONTIG sections

Scott Cain cain.cshl at gmail.com
Wed Sep 24 18:00:35 EDT 2008

Hi all,

The BioPerl script bp_genbank2gff.pl, which will either convert a
Genbank record to GFF or load it directly to a Bio::DB::GFF database,
is choking on GenBank records with CONTIG sections.  Since I don't
think these would ever be useful for generating GFF or loading into a
database (ie, the user will want to get all of the features on the
parts, not know what the parts are), is there a way to force a
Bio::DB::WebDBSeqI/Bio::DB::BioFetch to get the full record (like
specifying view=gbwithparts in the url at ncbi)?


Scott Cain, Ph. D. cain.cshl at gmail.com
GMOD Coordinator (http://gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory

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