percolator
commented
6 years ago Thanks for the patch, Mark! I appreciate your help.
On Fri, Feb 23, 2018 at 4:06 PM, userbz notifications@github.com wrote:
@userbz approved this pull request.
The logic is clear to me.
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Lukas Käll http://kaell.org Royal Institute of Technology - KTH Science for Life Laboratory School of Biotechnology Box 1031, 171 65 Solna, Sweden +46 8 790 9852 or +46 76 9425179
It seems that there are some nonsense iterations in fast_farms function when "psi" and "lambda" stop changing at some point of cycle.
Also there are "np.diag(C)" and "min_noise ** 2" operations inside the cycle which are never changed.
Please check the changes carefully, because due to the issue with reproducibility I've raised, it is hard to test properly the new changes.
On my testing dataset with 12 runs and 30k peptides the script processing time was reduced by 45% (Without MC simulation option)