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path: root/gn3/computations/gemma.py
AgeCommit message (Expand)Author
2023-10-27Remove reimport "Optional"....* gn3/computations/gemma.py: Delete reimport "Qptional". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Make implicit optional type hints PEP 484 compliant....Ran the command: pipx run no_implicit_optional ./ in the root directory. Munyoki Kilyungi
2023-10-26Fix errors caught by mypy.Frederick Muriuki Muriithi
2022-02-24gn3: Explicitly specify UTF-8 to be the file encoding....When the encoding is not specified explicitly, the system default encoding is used. This is not recommended. * gn3/computations/ctl.py (call_ctl_script), gn3/computations/gemma.py (generate_pheno_txt_file), gn3/computations/parsers.py (parse_genofile), gn3/computations/partial_correlations.py (partial_correlations_fast), gn3/computations/rqtl.py (process_rqtl_output, process_perm_output), gn3/computations/wgcna.py (dump_wgcna_data, call_wgcna_script), gn3/fs_helpers.py (jsonfile_to_dict): Explicitly specify UTF-8 to be the file encoding. * tests/unit/computations/test_gemma.py (TestGemma.test_generate_pheno_txt_file), tests/unit/computations/test_wgcna.py (TestWgcna.test_create_json_file): Test for call to open with encoding='utf-8' argument. Arun Isaac
2021-05-13Rename file_utils to fs_helpers...Generally avoid naming things with a "utils" prefix/ suffix since it encourages contributors to dump any new functions there; and over time, as the code grows, things get messy... BonfaceKilz
2021-03-10Fix k-compute command when "loco" is trueBonfaceKilz
2021-03-08Remove unused importsBonfaceKilz
2021-03-08Delete "generate_gemma_computation_cmd"BonfaceKilz
2021-03-08Add generic fn for computing k and gwa valuesBonfaceKilz
2021-03-08Apply pep-8 formatting...Began using elpy's format code fn BonfaceKilz
2021-03-08Move "generate_random_n_string" to file_utils...* gn3/computations/gemma.py (generaten_random_n_string): Move to... * gn3/file_utils.py: ... here. BonfaceKilz
2021-03-08Fix failing testsBonfaceKilz
2021-02-24Create a new helper function for generating k_values and GWABonfaceKilz
2021-02-24Add procedure that checks whether a list of paths existBonfaceKilz
2021-02-24Check if phenotype exists before creating oneBonfaceKilz
2021-02-24Add new procedure that computes the hash of an array of stringsBonfaceKilz
2021-02-24Add mypy-typing to function...* gn3/computations/gemma.py (generate_random_n_string): Add typing to function. BonfaceKilz
2021-02-24Append random 6 chars to generated phenotype fileBonfaceKilz
2021-02-24Create a new method for generating a valid phenotype file on the flyBonfaceKilz