[Biopython-dev] Bio.GFF and Brad's code

Brad Chapman chapmanb at 50mail.com
Thu Dec 3 14:25:34 UTC 2009

Hi Michiel;

> > If I crank that out what do we think about putting it in
> > with the __init__.py modifications I suggested?
> I'd definitely welcome a GFF parser in Biopython, but I think the
> current code needs to be simplified and its usage more consistent
> with other Biopython modules. It's great that the documentation is
> available. It's a big help in designing the module, in particular what
> its usage looks like to the user.

Awesome. I welcome these suggestions; it's really helpful to have
fresh eyes looking at it. Hopefully moving it into Biopython will
stimulate that.

> Let's start from basic GFF parsing. This is the example in the documentation:
> What is the purpose of creating the parser first, and then calling
> parser.parse on the in_handle? I'd much rather have
> >>> from BCBio import GFF
> >>> in_file = "your_file.gff"
> >>> in_handle = open(in_file)
> >>> for rec in GFF.parse(in_handle):
> ...    print rec
> >>> in_handle.close()

Great -- done for parsing and writing and committed to GitHub. The
documentation is updated as well.

Happy to get other comments and thoughts. Thanks again,

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