Interesting. FWIW, the fasta parser in bx has had little effort put into optimization (Bob Harris did some). The nib and 2bit parsers are hopefully where it shines.
It'd be really cool to compare some of the other features like IntervalIndexFile vs. NLMSA. I've not had time to do it, but it might be interesting (and encourage one or all of us to do some optimization ;). On Feb 11, 2009, at 2:38 PM, Istvan Albert wrote: > > > I have been long interested in comparing some of the performance > numbers across bioinformatics frameworks. Yesterday Jenny brought this > up, that gave me the push to see some numbers for myself. > > Below find some comparison numbers for fasta parsing, iteration, > sequence slicing, reverse complement for 4 bioinformatics frameworks: > > Pygr: http://code.google.com/p/pygr/ > Biopython: http://biopython.org/wiki/Main_Page > BX Python: http://bx-python.trac.bx.psu.edu/ > PyCogent: http://pycogent.sourceforge.net/ > > Here are the results: > http://code.google.com/p/pygr/source/browse/contrib/compare/results.txt > > The code: > http://code.google.com/p/pygr/source/browse/contrib/compare/benchmark.py > > Guess what the numbers were ... here is summary: > > ============================= > > *** benchmarking=data/100K.fasta > > Test Time > pygr_parse_fasta 5.7s > bio_parse_fasta 24.8s > bx_parse_fasta 28.8s > cogent_parse_fasta 56.1s > -------------------- > pygr_iter 14.5s > bio_iter 6.7s > bx_iter 5.8s > cogent_iter 8.2s > -------------------- > pygr_slice 11.8s > bio_slice 1.4s > bx_slice 0.8s > cogent_slice 11.9s > -------------------- > pygr_reverse_comp 35.6s > bio_reverse_comp 12.4s > bx_reverse_comp 8.1s > cogent_reverse_comp 44.4s > > ======================================== > > *** benchmarking=data/dm.fasta > > Test Time > pygr_parse_fasta 36.6s > bio_parse_fasta 17.7s > bx_parse_fasta 29.1s > cogent_parse_fasta 40.2s > -------------------- > pygr_iter 0.0s > bio_iter 3.0s > bx_iter 2.9s > cogent_iter 2.9s > -------------------- > pygr_slice 11.5s > bio_slice 1.4s > bx_slice 0.8s > cogent_slice 12.1s > -------------------- > pygr_reverse_comp 137.8s > bio_reverse_comp 5.3s > bx_reverse_comp 31.7s > cogent_reverse_comp 26.6s > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
