From cb2ab69689fa40f18af7e4e628baaaba61326ad6 Mon Sep 17 00:00:00 2001 From: Samuel Lee Date: Wed, 24 Mar 2021 09:08:50 -0400 Subject: [PATCH] Removed mapping error rate from estimate of denoised copy ratios output by gCNV and updated sklearn. --- scripts/gatkcondaenv.yml.template | 2 +- .../hellbender/gcnvkernel/models/model_denoising_calling.py | 3 +-- .../utils/python/PythonEnvironmentIntegrationTest.java | 2 +- 3 files changed, 3 insertions(+), 4 deletions(-) diff --git a/scripts/gatkcondaenv.yml.template b/scripts/gatkcondaenv.yml.template index 6d3f286a667..e2e283dc600 100644 --- a/scripts/gatkcondaenv.yml.template +++ b/scripts/gatkcondaenv.yml.template @@ -38,7 +38,7 @@ dependencies: # if you wish to update, note that versions of conda-forge::keras after 2.2.5 # undesirably set the environment variable KERAS_BACKEND = theano by default - defaults::intel-openmp=2019.4 -- conda-forge::scikit-learn=0.22.2 +- conda-forge::scikit-learn=0.23.1 - conda-forge::matplotlib=3.2.1 - conda-forge::pandas=1.0.3 diff --git a/src/main/python/org/broadinstitute/hellbender/gcnvkernel/models/model_denoising_calling.py b/src/main/python/org/broadinstitute/hellbender/gcnvkernel/models/model_denoising_calling.py index f5d525ace74..cefebd1cf2b 100644 --- a/src/main/python/org/broadinstitute/hellbender/gcnvkernel/models/model_denoising_calling.py +++ b/src/main/python/org/broadinstitute/hellbender/gcnvkernel/models/model_denoising_calling.py @@ -786,8 +786,7 @@ def __init__(self, # the expected number of erroneously mapped reads mean_mapping_error_correction_s = eps_mapping * read_depth_s * shared_workspace.average_ploidy_s - denoised_copy_ratio_st = ((shared_workspace.n_st - mean_mapping_error_correction_s.dimshuffle(0, 'x')) - / ((1.0 - eps_mapping) * read_depth_s.dimshuffle(0, 'x') * bias_st)) + denoised_copy_ratio_st = shared_workspace.n_st / (read_depth_s.dimshuffle(0, 'x') * bias_st) Deterministic(name='denoised_copy_ratio_st', var=denoised_copy_ratio_st) diff --git a/src/test/java/org/broadinstitute/hellbender/utils/python/PythonEnvironmentIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/utils/python/PythonEnvironmentIntegrationTest.java index fe89b721a1a..b055d8461cd 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/python/PythonEnvironmentIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/python/PythonEnvironmentIntegrationTest.java @@ -25,7 +25,7 @@ public Object[][] getDataPackagePresent() { { "pymc3", "3.1" }, { "keras", "2.2.4" }, { "h5py", "2.10.0" }, - { "sklearn", "0.22.2.post1" }, + { "sklearn", "0.23.1" }, { "matplotlib", "3.2.1" }, { "pandas", "1.0.3" }, { "argparse", null },