[Biopython-dev] Bio.GenBank (was: Bio.File)

Michiel de Hoon mjldehoon at yahoo.com
Wed Sep 14 15:34:01 UTC 2011

Hi Peter,

--- On Mon, 9/12/11, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> How's this?
> https://github.com/biopython/biopython/commit/ff72037efbae2da6eb6db550aa6d02b883ec1345

The code looks good.
About the documentation, at the top of the module you say that using Bio.GenBank can be useful for WGS master records. That is true, but people with particular interests may have other reasons to use Bio.GenBank, and maybe WGS master records will not be stored as GenBank files in the future. So it may be good to keep the documentation a bit more generic, so it's still valid in a few years. But I agree that in most cases and for most users, Bio.SeqIO is the appropriate module rather than Bio.GenBank.
Does Bio.SeqIO still need to use Bio.GenBank's FeatureParser? Or can it also use Bio.GenBank.read() or Bio.GenBank.parse()?


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