[Biopython-dev] New stuff in CVS

[Brad Chapman]

Hey Jeff, et al;
I noticed a new c-extension was added to the setup.py file, which is
supposed to be living in:

Bio/Tools/Statistics/cstathelpermodule.c

but it doesn't look like it actually got checked in. Not sure if this
is just an oversight, or if it just isn't ready yet...

Also, I noticed the download_many function added to Bio.GenBank. Very
useful stuff. If you want to work more on some of the stuff you
mention in the comments, like checking that all GIs are valid and
stuff like that, I have some code which does sort of similar stuff,
although I do it in a different way -- my code was meant to start with 
a list of accession numbers and retrieve all of the records in GenBank 
from that (I use it to automatically update my local copy o' the
Arabidopsis genome). So it doesn't start directly with GIs like yours.

If you want to check it out/steal some code or whatever, it's at:

http://bioinformatics.org/cgi-bin/cvsweb.cgi/biopy-pgml/Bio/PGML/Organize/FileFactory.py?rev=1.3&content-type=text/x-cvsweb-markup

(sorry about the long URL).

Also, along the same lines, I added some other KeyError conditions to
NCBIDictionary which I  ran into while I was working on this. The two
other things I ran into were getting back:

Please try again later. Server error  for GI "7212005"

and:

The sequence has been intentionally withdrawn : GI "9993999"

The first just happens randomly (whenever NCBI isn't happy, I guess),
and the second will happen if there are some cross-refs between the
old record and the new one. You'd get back the withdrawn GI first and
the new, good GI second, so if there wasn't an error than you'll end
up with the withdrawn "record" instead of the good one.

Just thought I'd mention it in case you see any other stuff along
these lines.

Thanks again for the new code!
Brad