[Bioperl-l] WGS file problems with Bio::SeqIO::genbank

[Chris Fields]

I'm currently working on a WGS file module for Bio::DB and noticed that,
although most WGS files (with the line WGS) are parsed normally, those that
have additional scaffolds (WGS_SCAFLD) are passed over.  These are with
regular WGS files and not the strange beast that is the WGS RefSeq file.

Example file AAAA000000 (O. sativa):
>From GenBank (direct from web site), FEATURES section:
------------------------------------------------------------------
FEATURES             Location/Qualifiers
     source          1..50231
                     /organism="Oryza sativa (indica cultivar-group)"
                     /mol_type="genomic DNA"
                     /cultivar="93-11"
                     /db_xref="taxon:39946"
WGS         AAAA02000001-AAAA02050231
WGS_SCAFLD  CM000126-CM000137
WGS_SCAFLD  CH398081-CH401163
//
------------------------------------------------------------------

Passed through SeqIO:
------------------------------------------------------------------
FEATURES             Location/Qualifiers
     source          1..50231
                     /db_xref="taxon:39946"
                     /mol_type="genomic DNA"
                     /cultivar="93-11"
                     /organism="Oryza sativa (indica cultivar-group)"
WGS         AAAA02000001-AAAA02050231

//
------------------------------------------------------------------
I'll post as a bug in Bugzilla for now.  I'm looking at Bio::SeqIO::genbank
and may post a fix when/if I can work out how SeqIO parses. 

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign