[Biopython-dev] GSoC SearchIO project

[Peter Cock]

On Tue, Apr 10, 2012 at 1:58 AM, Brad Chapman wrote:
> Michiel;
>> Hi Eric, Peter,
>>
>> > How about Bio.Search, for now?
>>
>> I would prefer Bio.Pairwise or Bio.Align.Pairwise, since that tells
>> users something about what the module is for. Bio.Search could be
>> anything (search PubMed? search the Entrez databases? search Google?
>> anyway Bio.Search does not suggest that this module is about pairwise
>> alignments). But Peter previously mentioned that he doesn't like
>> Bio.Pairwise; can we convince you?
>
> I agree with Peter on this one. The module is primarily about searching
> a sequence database with an input via multiple methods, not about
> pairwise alignment of two sequences with is what Bio.Align.Pairwise
> suggests to me.
>
> Brad

On potential problem with Bio.Search (on top of concerns raised
here about vagueness) Bow and I were just talking about during
our weekly GSoC video call was the existence of Bio/Search.py
which is obsolete and long overdue for removal. I have just
deprecated it (something I forgot to do before the last release):
https://github.com/biopython/biopython/commit/5a275ccd1df3def40df1eef517af755d373dadd8

We'd earlier talked about using Bio.Search as the namespace. I was
worried about the potential existence on a user's machine of both
Bio/Search.py (the old obsolete code) and Bio/Search/__init__.py
(aka SearchIO, the new module) and which would take precedence
when doing: from Bio import Search

Given how Python module installations work, that seems highly
likely to occur. The good news is that the package would take
priority - see http://www.python.org/doc/essays/packages.html

>>>> What If I Have a Module and a Package With The Same Name?
>>>>
>>>> You may have a directory (on sys.path) which has both a module
>>>> spam.py and a subdirectory spam that contains an __init__.py
>>>> (without the __init__.py, a directory is not recognized as a package).
>>>> In this case, the subdirectory has precedence, and importing spam
>>>> will ignore the spam.py file, loading the package spam instead. If
>>>> you want the module spam.py to have precedence, it must be
>>>> placed in a directory that comes earlier in sys.path.

So there is no technical reason to avoid Bio.Search as an
option for the Bio.SearchIO namespace. We could then
have Bio.Search.Applications for command line wrappers,
consistent with Bio.Phylo.Applications, Bio.Motif.Applications
and Bio.Align.Applications.

Of course, Bio.Search is still perhaps too broad a name... but
on balance perhaps it is still better than Bio.SearchIO?

Regards,

Peter