[Biopython] Fasta.index_file: functionality removed?

[Peter]

On Thu, Jun 18, 2009 at 11:00 AM, Peter wrote:
> On Thu, Jun 18, 2009 at 2:13 AM, Michiel de Hoon wrote:
>>
>> For the short term, the easiest solution for you is probably to pick up
>> Bio.Fasta from an older version of Biopython.
>
> Note you would also need Martel and Mindy (still included in Biopython
> 1.50, but won't be in Biopython 1.51), and ideally mxTextTools 2.0 (not
> mxTextTools 3.0).

Thinking about it, we might be able to resurrect the Bio.Fasta.index_file
function and Dictionary class using Bio.Index which IIRC is what it used
to use instead of Martel/Mindy (this is still used in Bio.SwissProt.SProt).
This would be a reasonable amount of work though...

On the other hand, I was going to propose we finally deprecate Bio.Fasta
in Biopython 1.51, given Bio.SeqIO has been the preferred way to read/
write FASTA files since Biopython 1.43 (March 2007). I wanted to phase
out Bio.Fasta gradually given this was once a very widely used part of
Biopython, and felt after two years as effectively obsolete it was time for
an official deprecation (with a warning message when imported).

Peter