genenetwork3/scripts, branch bugfix/remove-pre-data-parsing GeneNetwork3 REST API for data science and machine learning http://git.genenetwork.org/genenetwork3/atom?h=bugfix%2Fremove-pre-data-parsing 2022-07-29T01:00:41+00:00 New script to run sample correlations 2022-07-29T01:00:41+00:00 Frederick Muriuki Muriithi 2022-07-29T01:00:41+00:00 urn:sha1:6b11a267084c131ac7e1be76c4eb602996fd829e * README.md: update mypy's invocation * scripts/argparse_actions.py: new file - implement custom FileCheck action for argparse * scripts/sample_correlations.py: new file - implement new script to run sample correlations in an external process Parse the method from UI before passing it to external process 2022-06-28T06:32:14+00:00 Frederick Muriuki Muriithi 2022-06-28T06:32:14+00:00 urn:sha1:d8d590cbc0a427c2f508c66bc91cd8af97aba606 To reduce the chances of the system failing due to the external process being launched with the wrong parameters, add a parsing stage that converts the method from the UI into a form acceptable by the CLI script. * gn3/commands.py: parse the method from UI * scripts/partial_correlations.py: simplify the acceptable methods Restrict partial correlation method choices 2022-06-20T08:17:11+00:00 Frederick Muriuki Muriithi 2022-06-20T08:17:11+00:00 urn:sha1:7f66bb029322a06b52359abf8836e158afaa6755 - Have "Pearson's r" and "Spearman's rho" as the only valid choices for the partial correlations Run partial correlations with external script 2022-05-24T11:19:57+00:00 Frederick Muriuki Muriithi 2022-05-24T11:19:57+00:00 urn:sha1:fdf9061981ce5d341d178951adeb19dd0376ee66 Use new external script to run the partial correlations for both cases, i.e. - against an entire dataset, or - against selected traits New script to compute partial correlations 2022-05-24T02:16:55+00:00 Frederick Muriuki Muriithi 2022-05-24T01:46:57+00:00 urn:sha1:36f8421a8fe223189ab88ee1df3923719ffa4fc0 * Add a new script to compute the partial correlations against: - a select list of traits, or - an entire dataset depending on the specified subcommand. This new script is meant to supercede the `scripts/partial_correlations.py` script. * Fix the check for errors * Reorganise the order of arguments for the `partial_correlations_with_target_traits` function: move the `method` argument before the `target_trait_names` argument so that the common arguments in the partial correlation computation functions share the same order. Extract common error checking. Rename function. 2022-05-05T12:19:08+00:00 Frederick Muriuki Muriithi 2022-05-05T12:19:08+00:00 urn:sha1:be9d1d4aad720274f6d75345123fae8d6a96bc12 * Extract the common error checking code into a separate function * Rename the function to make its use clearer Merge branch 'feature/add_rqtl_pairscan' of https://github.com/zsloan/genenetwork3 into feature/add_rqtl_pairscan 2022-03-22T20:39:22+00:00 zsloan 2022-03-22T20:39:22+00:00 urn:sha1:a75634cc5637168165e601f09dc9ad820e6e443f Change order of if statements for running genoprob command 2022-03-22T20:28:58+00:00 zsloan 2022-03-22T20:28:58+00:00 urn:sha1:0e6990940e22eb0431d6a27e45d29bc04d8ad582 Now it checks for pairscan first, just in case interval ends up being passed (which is an irrelevant parameter for pairscan) Also added a couple more verbose prints Updated rqtl_wrapper to also return a map file when doing a pair-scan (since we need the list of markers/pseudomarkers and their positions) 2022-03-22T19:08:01+00:00 zsloan 2021-08-02T21:07:52+00:00 urn:sha1:4c3359082fbb1eef93a9e54c633f938606cba5f6 Added line priting pair-scan results to CSV and changed the default step-size to 10cM for pair-scan 2022-03-22T19:07:00+00:00 zsloan 2021-07-23T20:08:36+00:00 urn:sha1:acfea0fc8793372723be0e64316002ed9bc2403b