[Biojava-l] RichSequence.IOTools performance

[Khalil El Mazouari]

Hi,

I just did some tests with FastaWriterHelper.writeSequence vs RichSequence.IOTools.writeFasta. Result was not expected!!

FastaWriterHelper.writeSequence: 37% of the execution time.
RichSequence.IOTools.writeFasta: 11.6% of the execution time.

In this test, 9733 protein seq were annotated and 6599 seq out to multiple fasta file. 

In my case at lease, biojavax is more performant than Biojava3.

Regards,

Khalil

PS: I AM NOT BENCHMARKING BIOJAVAX VS BIOJAVA3!!!


On 28 Mar 2011, at 18:53, Scooter Willis wrote:

> Khalil
> 
> Biojava3 has significant speed improvements as a complete rewrite of
> BioJava 1.7 but does not contain the same feature and functions. You
> can do some testing with BioJava3 to see if you find the increased
> performance and add port/write the code for the file formats you need
> to support.
> 
> Thanks
> 
> Scooter
> 
> On Mon, Mar 28, 2011 at 12:07 PM, Khalil El Mazouari
> <khalil.elmazouari at gmail.com> wrote:
>> Hi,
>> 
>> I am developing a sequence annotation app. It should handle ± 100.000 sequence per run.
>> 
>> When profiling the app (with 10.000 seq), the total execution time was ± 20 seconds, of which 57% was used for   RichSequence.IOTools.writeGenbak!!
>> 
>> How one could improve the RichSequence.IOTools performance?
>> 
>> Thanks.
>> 
>> khalil
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>> 
>>