[Biopython-dev] Indexing (large) sequence files with Bio.SeqIO

[Peter]

On Tue, Sep 8, 2009 at 2:53 PM, Peter wrote:
> On Tue, Sep 8, 2009 at 2:30 PM, Michiel de Hoon wrote:
>>  On Tue, 9/8/09, Peter wrote:
>>> Did you have any ideas for a better name than
>>> Bio.SeqIO.indexed_dict()?
>>
>> Is indexed_dict a function? If so, I suggest we use a verb instead
>> of a noun. Maybe just "index"?
>
> Bio.SeqIO.indexed_dict() is a function which returns a dictionary like
> object. So yes, a verb would be better, and "index" is short and sweet.

Any other comments? Otherwise I'll switch Bio.SeqIO.indexed_dict()
to Bio.SeqIO.index() for the next release.

Thinking ahead, in addition to the current code (indexing a file, keeping
the index in memory) we might in future add want to something like
Bio.SeqIO.sqlite_index() where the index is kept in a database etc.

Peter