[Biopython] Indexing large sequence files

[Cedar McKay]

I used the latest multi-format aware version you posted. Using the old  
technique, it took 57 minutes (vs 13 minutes the new way), so we see  
quite an improvement. Thanks,
Cedar


On Jun 24, 2009, at 9:12 AM, Peter wrote:

> On Tue, Jun 23, 2009 at 10:14 PM, Cedar  
> McKay<cmckay at u.washington.edu> wrote:
>>
>> I gave your code a shot, and it worked great! My script took 13  
>> minutes to
>> run, which is a lot better than before, when it would die from lack  
>> of
>> memory. Thanks a lot!
>>
>> Cedar
>
> Great :)
>
> Was it the FASTA only version, or the more generic one you tried?
> (I would expect the times to be about the same from my limited
> benchmarking).
>
> Did you have an old version of the script using Bio.Fasta.index_file
> from Biopython 1.43? How long did that take?
>
> Peter