[Biopython-dev] Bio.Entrez / next Biopython release.

[Peter]

Michiel de Hoon wrote:
> Hi everybody,
>
>  As discussed previously, I created a module Bio.Entrez for interacting
> with NCBI's Entrez databases ... The code is now in CVS as Bio/Entrez.py.
> In hindsight, it would probably have been a better idea to use
> Bio/Entrez/__init__.py in case we want to expand Bio.Entrez, but
> anyway this can be rectified before creating the next Biopython release.

I agree with you on the use of Bio/Entrez/__init__.py

>  I also wrote some documentation for Bio.Entrez. You can have
> a preview at http://biopython.org/DIST/docs/tutorial/Tutorial-proposal.html;
> Chapter 6 describes Bio.Entrez, and gives a good overview of the current
> status of this module.

Great.

>  The module Bio.Entrez was created in response to Bug #2393:
>  http://bugzilla.open-bio.org/show_bug.cgi?id=2393
>  Using Bio.Entrez, we can fix this bug easily, and then create a new release.

Good.

> This is one thing to consider though:
>  Like Bio.WWW.NCBI, Bio.Entrez provides access to NCBI's Entrez
> databases but does not provide parsers for the output generated by NCBI
> (note: some file formats generated by NCBI Entrez' sequence databases
> can be parsed by Bio.SeqIO). Our options are then:
>  1) Keep Bio.Entrez as a module only to access NCBI Entrez, but not to parse the results.
>  2) Add parsers to Bio.Entrez.
>  3) Make a new Biopython release now, and potentially add parsers later.
>
>  Suggestions, preferences, comments, anybody?

I would go with option (3), and make a new release soon.  If we write any Entrez
specific parsers, they could live in Bio.Entrez

Peter