[Bioperl-l] GenBank accession bug?

Dave Messina dmessina at wustl.edu
Thu Feb 22 15:53:01 EST 2007


> The issue at hand is whether we can support GenBank accessions/
> display_id/version with your naming scheme.

Chris, I'm a little unsure of what you're saying here (which might mean
that you're already saying what I'm about to...say). Do you mean it might
be tricky to support both the Genbank standard and Dmitry's
simultaneously?

I would argue any arbitrary ID should be supported as long as that ID is a
contiguous non-space word (\S+).

Actually the existing accession regex looks like it already supports IDs
with '-':

/^ACCESSION\s+(\S.*\S)/

It's only the version regex which doesn't (\w doesn't include '-'):

/^\w+\.(\d+)/


Anyone else have thoughts or comments on this? Off the top of my head, I
can't think of any issues that might arise from doing so (apart from
having to modify all of the SeqIO modules to support it).

Dave





More information about the Bioperl-l mailing list