[Bioperl-l] Changes to NCBIHelper (RE: CONTIG, genome files)

[Chris Fields]

I committed a change to NCBIHelper that permits the downloading of CON
(contig) files and corrects an issue where no sequence features were saved
when rebuilding those files.  If you use Bio::DB::GenBank regularly to
download genome files, this likely will NOT affect your code unless you
explicitly set the format type to 'genbank', like so:

$factory = Bio::DB::GenBank->new(-format => 'gb'); # or 'genbank'

I believe most will not have that setting since the default was already
'gb'.  Now, the default is 'gbwithparts', which returns the full sequence
regardless.  If it is a file with a CONTIG line, the sequence is built on
NCBI's end and will include seq features if they are present).  As Brian
said, we'll let NCBI do the work for us!  

If you need the actual file w/o sequence, then you can set the format to
'genbank' (like above) and it will grab it for you.  There was an unrelated
problem with CONTIG line parsing that I also fixed, where I changed the
format over to a Bio::Annotation::SimpleValue as a workaround for now; for
some reason some CON files were misparsed and resulted in infinite loops or
missing 'join' statements.  

Chris

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