diff --git a/MANIFEST.in b/MANIFEST.in index ac2af8ff93547e9a0b30bc6bc4b3c0294c613cf2..2f44dbf82157a6e81e14acf9fd7c3ae8998a3ca4 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,5 +1,5 @@ include README.md include setup.cfg include jass/swagger/swagger.yaml -recursive-include jass/static * -recursive-include celery_files * +recursive-include jass/models/data/ *.tsv +recursive-include jass/static * \ No newline at end of file diff --git a/jass/models/data/coef_mean_model.tsv b/jass/models/data/coef_mean_model.tsv new file mode 100644 index 0000000000000000000000000000000000000000..ca07eb89886c598f96afb4e4f998f870e57d30f1 --- /dev/null +++ b/jass/models/data/coef_mean_model.tsv @@ -0,0 +1,7 @@ + 0 +k_coef_mv 0.07740334977380119 +log10_avg_distance_cor_coef_mv -0.6999110771883902 +log10_mean_gencov_coef_mv 0.746794584985343 +avg_Neff_coef_mv 0.07289261717080556 +avg_h2_coef_mv -0.516496395500929 +avg_perc_h2_diff_region_coef_mv 0.15727591593399 diff --git a/jass/models/data/range_feature_gain_prediction.tsv b/jass/models/data/range_feature_gain_prediction.tsv new file mode 100644 index 0000000000000000000000000000000000000000..30c63afb46258403eeb27bf17cb6a9095afbd972 --- /dev/null +++ b/jass/models/data/range_feature_gain_prediction.tsv @@ -0,0 +1,7 @@ + minimum_value maximum_value +k 2.0 12.0 +log10_avg_distance_cor -4.675617219570908 0.20864138105896807 +log10_mean_gencov -4.4093921991254446 -0.46117501106209624 +avg_Neff 6730.5 697828.0 +avg_h2 0.014033707225812 0.4361454950334251 +avg_perc_h2_diff_region 0.0906544694784672 0.9831222899777692 diff --git a/jass/models/gain.py b/jass/models/gain.py index d92db8fec2befc4f099bc26c4ae05b26eb230c40..b0cef418e986c6a041b520dac976a061f1c32f5a 100644 --- a/jass/models/gain.py +++ b/jass/models/gain.py @@ -1,10 +1,14 @@ +import pkg_resources import pandas as pd import numpy as np - +import os # data issued from https://doi.org/10.1101/2023.10.27.564319 -X_range = pd.read_csv("./data/range_feature_gain_prediction.tsv", sep="\t", index_col=0) -model_coefficients = pd.read_csv("./data/coef_mean_model.tsv", sep="\t", index_col=0) +stream = pkg_resources.resource_stream(__name__, 'data/range_feature_gain_prediction.tsv') +X_range = pd.read_csv(stream, sep="\t", index_col=0) + +stream = pkg_resources.resource_stream(__name__, 'data/coef_mean_model.tsv') +model_coefficients = pd.read_csv(stream, sep="\t", index_col=0) # Scale according to observed def scale_feature(X, feature_name): diff --git a/jass/test/data_real/initTable-computed-cov.hdf5 b/jass/test/data_real/initTable-computed-cov.hdf5 index 09c727c19fe74d47c8b6c4d5ca482d2c899a37b6..e5c9e418f87eb525bc9f2a0b329427c11967fa4f 100644 Binary files a/jass/test/data_real/initTable-computed-cov.hdf5 and b/jass/test/data_real/initTable-computed-cov.hdf5 differ diff --git a/jass/test/data_real/initTable.hdf5 b/jass/test/data_real/initTable.hdf5 index 85a869ff55510f47b6622db2a0c81bfa8e904be5..bbeb66410fbcbb9dcbfaf5dae49355d0b9018cf9 100644 Binary files a/jass/test/data_real/initTable.hdf5 and b/jass/test/data_real/initTable.hdf5 differ diff --git a/jass/test/data_real/worktable-nonans.hdf5 b/jass/test/data_real/worktable-nonans.hdf5 index 2e1f6526b9f5f2741ed7627bb6f72e12e543ae4f..1323e8187a7012c6351c40f382733e0cf9540554 100644 Binary files a/jass/test/data_real/worktable-nonans.hdf5 and b/jass/test/data_real/worktable-nonans.hdf5 differ diff --git a/jass/test/data_real/worktable-withnans.hdf5 b/jass/test/data_real/worktable-withnans.hdf5 index 6c0162e61d22b93316dfe293a05b5b47d6c68fe4..809f790a23140377941366ffc081c41dfd0e4e97 100644 Binary files a/jass/test/data_real/worktable-withnans.hdf5 and b/jass/test/data_real/worktable-withnans.hdf5 differ diff --git a/setup.py b/setup.py index f219c359653ae00d87b9dfacea28330db078ba1f..61bba8e85879dc9f5f6e8efca8c09667813475b9 100644 --- a/setup.py +++ b/setup.py @@ -31,7 +31,7 @@ setup( install_requires=REQUIRES, license="MIT", keywords=["GWAS", "Data analysis", "summary statistics"], - package_data={'jass': ['swagger/swagger.yaml']}, + package_data={'jass': ['swagger/swagger.yaml', "data/*.tsv"]}, include_package_data=True, long_description=readme, long_description_content_type="text/markdown",