| Age | Commit message (Expand) | Author |
|---|
| 2022-02-24 | gn3: 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 |
| 2021-05-13 | Rename 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 |
| 2021-03-10 | Fix k-compute command when "loco" is true | BonfaceKilz |
| 2021-03-08 | Remove unused imports | BonfaceKilz |
| 2021-03-08 | Delete "generate_gemma_computation_cmd" | BonfaceKilz |
| 2021-03-08 | Add generic fn for computing k and gwa values | BonfaceKilz |
| 2021-03-08 | Apply pep-8 formatting...Began using elpy's format code fn
| BonfaceKilz |
| 2021-03-08 | Move "generate_random_n_string" to file_utils...* gn3/computations/gemma.py (generaten_random_n_string): Move to...
* gn3/file_utils.py: ... here.
| BonfaceKilz |
| 2021-03-08 | Fix failing tests | BonfaceKilz |
| 2021-02-24 | Create a new helper function for generating k_values and GWA | BonfaceKilz |
| 2021-02-24 | Add procedure that checks whether a list of paths exist | BonfaceKilz |
| 2021-02-24 | Check if phenotype exists before creating one | BonfaceKilz |
| 2021-02-24 | Add new procedure that computes the hash of an array of strings | BonfaceKilz |
| 2021-02-24 | Add mypy-typing to function...* gn3/computations/gemma.py (generate_random_n_string): Add typing to function.
| BonfaceKilz |
| 2021-02-24 | Append random 6 chars to generated phenotype file | BonfaceKilz |
| 2021-02-24 | Create a new method for generating a valid phenotype file on the fly | BonfaceKilz |
