| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-09-12 | Fix pylint errors. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-09-12 | From gn3 only use TMPDIR/gn3 paths | Pjotr Prins | |
| 2024-09-12 | Replace TMPDIR/output with TMPDIR/gn3 so it is clear where it comes from | Pjotr Prins | |
| 2024-09-12 | Make sure TMPDIR directories exist! | Pjotr Prins | |
| 2024-09-12 | Getting Rqtl to run on fallback | Pjotr Prins | |
| 2023-01-25 | Some comments | Pjotr Prins | |
| 2022-03-23 | Run python-black on file and fix other pylint issues. | BonfaceKilz | |
| See: <https://ci.genenetwork.org/jobs/genenetwork3-pylint/126> * gn3/computations/rqtl.py: Run `black gn3/computations/rqtl.py`. Also, manually fix other pylint issues. | |||
| 2022-03-22 | Fixes pylint errors | zsloan | |
| 2022-03-22 | Fixed mypy typing errors | zsloan | |
| 2022-03-22 | Tried to make the docstrings more consistent | zsloan | |
| 2022-03-22 | Add typing to some functions | zsloan | |
| 2022-03-22 | Add functions for getting proximal/distal markers for each pseudomarker ↵ | zsloan | |
| position in pair-scan results + return only the sorted top 500 results | |||
| 2022-03-22 | Added genofile name to inputs for processing R/qtl pair-scan results, since ↵ | zsloan | |
| it's needed to store the proximal/distal markers for each position | |||
| 2022-03-22 | Removed quotes from beginning and end of chromosome string | zsloan | |
| 2022-03-22 | Fixed a cople function calls to use the updated function names | zsloan | |
| 2022-03-22 | Create pairscan_for_figure and pairscan_for_table functions that return the ↵ | zsloan | |
| Dict and List respectively used for the pair scan figure and the table showing the results | |||
| 2022-03-22 | Added pairscan boolean kwarg and process_rqtl_pairscan function for reading ↵ | zsloan | |
| in pairscan results + renamed process_rqtl_output to process_rqtl_mapping to distinguish between that and pairscan | |||
| 2022-02-24 | gn3: Explicitly specify UTF-8 to be the file encoding. | Arun Isaac | |
| 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. | |||
| 2021-06-18 | Fixed pylint issues | zsloan | |
| 2021-06-18 | Resolve mypy errors in computations/rqtl.py | zsloan | |
| 2021-05-25 | Include code that processes rqtl output files and returns actual results ↵ | zsloan | |
| instead of just the output filename | |||
| 2021-05-19 | Temporarily replace forward-slashes with underscores, since they can be ↵ | zsloan | |
| included in the hashes used for filenames | |||
| 2021-05-18 | Fixed generate_rqtl_cmd to make the kwarg hash from a combination of ↵ | zsloan | |
| keywords and arguments + account for boolean kwargs without values (like --interval or --covar) | |||
| 2021-05-18 | Fixed variety of issues detected by pylint | zsloan | |
| 2021-05-17 | Created compose_rqtl_command and generate_rqtl_command to create the actual ↵ | zsloan | |
| command to be run from the command line; used the same pattern as for GEMMA for consistency | |||
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index : genenetwork3 | |
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