genenetwork3 - GeneNetwork3 REST API for data science and machine learning

Age	Commit message (Collapse)	Author
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