[BioPython] script to extract records from nucleotide database

[Peter]

> Thanks for all the comments, so since you said you removed Bio.FormatIO in
> version 1.44 and replaced it with Bio.SeqIO do you think I can still
> successfully use that code I was given if I have 1.44 provided I watch out
> for bugs and so on?

Assuming you can apply the fix for Bug 2393, then that
Bio.GenBank.NCBIDictionary code should work fine with Biopython 1.44.

There is also a related example in the SeqIO chapter of the tutorial
using the Bio.GenBank.download_many() function.

> What is the difference between Bio.FormatIO and
> Bio.SeqIO, other then them describing file formats differently?

In terms of typical end use, Bio.SeqIO and Bio.FormatIO provided
similar capabilities, but FormatIO wasn't very up to date in terms of
its format support.  The big differences are internal.  For any new
code, please try Bio.SeqIO (available in Biopython 1.43 onwards),
which is described in the tutorial and the wiki:
http://biopython.org/wiki/SeqIO

> Also how exactly could one have a partial installation, some of the package not
> installing?

This was a guess - there is/was clearly something odd about your
install.  If you installed from source, maybe some step failed part
way leaving you with only some parts installed.  Another possibility
is on BSD is there is something different about the installation paths
which is confusing things.  We haven't worked out what went wrong on
your system so I'm was just speculating.

Peter