[Bioperl-l] WGS, WGS_SCAFLD support added for GenBank files

Chris Fields cjfields at uiuc.edu
Thu Mar 9 13:08:16 EST 2006

Added WGS and WGS_SCAFLD support to Bio::SeqIO::genbank as well as tests and
WGS sample file; the previous fix missed the WGS_SCAFLD line.  I will also
soon add support to Bio::DB::GenBank for downloading WGS and WGS_SCAFLD

Brian, I found a pretty decent speed improvement for contig building in
Bio::DB::NCBIHelper; it basically fetches the contig whole from NCBI using
return type of 'gbwithparts' so the work is done on their end and just
switches the CONTIG line with the sequence; it took about 10 seconds vs. ~50
seconds using an unmodified NCBIHelper on my PC.  I haven't committed it yet
bc I noticed the resulting contig files differ; the bioperl contig build
lacks any N's from the 'gaps()' in the CONTIG line while NCBI's version has
the N filler.  I didn't know if the difference was a bug or not.  Should I
go ahead and commit?

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

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