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

[Peter]

On Wed, Sep 16, 2009 at 2:48 PM, Peter wrote:
> 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.

Done in CVS.

> 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