Added support for NetMHCstabpan (GH Issue #64) #167
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Thanks for this contribution @dhuvik . Looks reasonable to me. Could you add a unit test for it? |
timodonnell
reviewed
Mar 12, 2024
tests/test_netmhc_stabpan.py
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| for i, (expected, actual) in enumerate(zip(web_server_predictions, stability_predictions)): | ||
| # Check to make sure that the stability predictions are within 0.01 of the webserver values. | ||
| # This could be the result of different versions of dependencies or the nature of the ANN itself. | ||
| approx_(expected, actual, tol=0.01, msg="Peptide %d: expected %f but got %f" % (i, expected, actual)) |
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I'd suggest using numpy.testing.assert_allclose here rather than writing your own function
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@dhuvik I've been mercilessly rolling my own testing helpers so might be setting a bad precedent but agree with Tim
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Thanks Tim! Will go ahead and make that change
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Also @timodonnell I still need to add a netmhc-bundle access token to secrets to make the GH Actions unit tests work, it's on my TODO list for this week. |
iskandr
reviewed
Mar 12, 2024
tests/common.py
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| @@ -24,6 +24,12 @@ def eq_(x, y, msg=None): | |||
| else: | |||
| assert x == y, msg | |||
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| def approx_(x, y, tol=1e-6, msg=None): | |||
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Want to oblige @timodonnell and call numpy.testing.assert_allclose here?
iskandr
approved these changes
Mar 13, 2024
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Files changed - 2
netmhcstabpan.py:
Added a NetMHCstabpan class that inherits from the BaseCommandlinePredictor parent class. The program_name is set to "netMHCstabpan". All other attributes are the same as as in other NetMHC* instances.
parsing.py:
Added a parse_netmhcstabpan function. Maps the Thalf_life to the score index, the identity to the key index, and the %Rank_Stab to the rank_index.