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 -~----------~----~----~----~------~----~------~--~---
