[Biopython-dev] Second go at GenBank parser

Jeffrey Chang jchang at SMI.Stanford.EDU
Fri Jan 12 01:06:11 EST 2001

On Tue, 9 Jan 2001, Brad Chapman wrote:

> Hi Jeff!
>    Thanks for getting back with me. Sorry I have been so slow. I was
> away over the break and then was so excited to code when I got back
> that I jumped right into to working hard-core on Biocorba (more on
> that fairly soon :-).

Yep, I know how that is.  I'm just getting back from break and am catching
up on my email.

> me:
> > > o Naming of modules -- right now my naming sucks (the "supplimentary"
> > > feature classes, like Location.py and Reference.py are in a module
> > > called 'FeatureInfo', for instance. yeck.), so if people have good
> > > ideas for how to name things I'll definately take 'em.
> Jeff:
> > Are these meant to be used with SeqFeatures?  If so, how about just
> > SeqFeature.Location and SeqFeature.Reference?
> Do you mean put them all in the SeqFeature.py module? That sounds like
> a fine solution to me (just wanted to be sure I understand you).

I think so.  If these are all classes that are to be used with
SeqFeatures, then that seems like a reasonable place to put it.

> > > Finally, I noticed Jeff put his snazzy code in GenBank/__init__.py --
> > > Should my GenBank.py go into __init__.py?
> >
> > Yes.  GenBank is a good name for it, and as per Andrew's earlier email, we
> > should avoid having code in both GenBank/__init__.py and
> > GenBank/GenBank.py.
> Okay, so you want me to integrate it with your __init__.py stuff? That
> is no problem just wanted to be sure. I definately want to avoid
> Andrew's __init__.py/GenBank.py-type problem.

Yep, integrate away!

> One thing -- I added the ability to index files as a Dictionary (a la
> the other Parsers). Is it too confusing to having Dictionary and
> NCBIDictionary in the same module? Just curious.

It's fine with me.  Anyone else?


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