added some utility codes #87
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LilySnow
commented
Jul 16, 2019
LilySnow
commented
- plot_utils.py: for plotting success rate and hit rate averaging over cases. compare with haddock scores.
- run_slurmFLs.py: submit slurm jobs by batches (one batch waiting for the first N batches to finish). Each job uses M cores in parallel.
- get_h5subset.py: extract a subset of docked models from one hdf5 to form a small test set.
Pull Request Test Coverage Report for Build 509
💛 - Coveralls |
…to successrate Trying to tidy up my code (security issue from subprocess) locally.
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Tried to use |
…to successrate added unitest for hitrate and success rate in plot_utils.py
split plot_utils to calcualtion and plot
deeprank/utils/count_hits.py
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| #!/usr/bin/env python | |||
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I will replace count_hits.py with my code for checking statistics including hits, which is more general.
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| #!/usr/bin/env python | |||
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Will be updated to be able to extract not only 5 but first N models.
deeprank/utils/get_subset.py
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| #!/usr/bin/env python | |||
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Will be deleted. It is same as get_h5subset.py.
test/test_hitrate_successrate.py
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| import unittest | |||
| from deeprank.utils.plot_utils import evaluate | |||
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CI failed due to the R_HOME problem from rpy2 package, but the tests passed locally. Could move the utility code to a new repo for only in-house using, considering these code are non-generic.
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rpy2 is not needed in unittest. Too many repos already ... At the current stage, we are the major users of deeprank.
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| import numpy as np | |||
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Extract the calculation of hit/success rate from plot_utils to this new file, which could avoid CI failure due to the import of rpy2 module.
