[BioPython] BioSQL documentation for Biopython

[Peter]

I've been away a few days, but it looks like you and Sebastian has
worked out where things had been going wrong.  Good job :)

>  > Everything went OK. I could follow the whole document. The only minor
>  > difference I found was:
>  >
>  >>>> print feature.location
>  > (0..880)
>  >
>  > It is in fact:
>  >
>  >>>> print feature.location
>  > [0:880]

That was a change made a year and a half ago - it is just cosmetic.
http://bugzilla.open-bio.org/show_bug.cgi?id=1902

>  >>  I'll be releasing within the next couple of days, so if this is
>  >>  outdated I'd like to remove it from (at least) the release branch.

As you'll have noticed, Biopython 1.44 has a few problems with BioSQL,
and the next release currently in CVS will be a lot better.  It might
be worth adding a warning to the BioSQL release for any Biopython
users to wait for Biopython 1.45.

The only other thing I noticed was this example code:

  >>> from Bio import GenBank
  >>> parser = GenBank.FeatureParser()
  >>> iterator = GenBank.Iterator(open("cor6_6.gb"), parser)

I would write this using Bio.SeqIO as we a promoting this as a uniform
sequence input/output library in Biopython (as in the wiki page
Sebastian mentioned).  i.e.

  >>> from Bio import SeqIO
  >>> iterator = SeqIO.parse(open("cor6_6.gb"), "genbank")

(However I have not yet sat down and gone through the whole document)

Peter