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2022-07-29New script to run sample correlations...* 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 Frederick Muriuki Muriithi
2022-06-28Parse the method from UI before passing it to external process...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 Frederick Muriuki Muriithi
2022-06-20Restrict partial correlation method choices...- Have "Pearson's r" and "Spearman's rho" as the only valid choices for the partial correlations Frederick Muriuki Muriithi
2022-05-24Run partial correlations with external script...Use new external script to run the partial correlations for both cases, i.e. - against an entire dataset, or - against selected traits Frederick Muriuki Muriithi
2022-05-24New script to compute partial correlations...* 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. Frederick Muriuki Muriithi
2022-05-05Extract common error checking. Rename function....* Extract the common error checking code into a separate function * Rename the function to make its use clearer Frederick Muriuki Muriithi
2022-03-22Merge branch 'feature/add_rqtl_pairscan' of https://github.com/zsloan/genenet...zsloan
2022-03-22Change order of if statements for running genoprob command...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 zsloan
2022-03-22Updated rqtl_wrapper to also return a map file when doing a pair-scan (since ...zsloan
2022-03-22Added line priting pair-scan results to CSV and changed the default step-size...zsloan
2022-03-22- Added scan_func function that determines whether scanone or scantwo...(pairscan) is used - For pairscan default to using step 20 (subject to change, but some step is required during calc.genoprob to make it run fast enough) - Added some new verbose prints zsloan
2022-03-22Added option for running pairscan to rqtl_wrapper.Rzsloan
2022-03-08Create database connections within context managers...Use the `with` context manager to open database connections, so as to ensure that those connections are closed once the call is completed. This hopefully avoids the 'too many connections' error Frederick Muriuki Muriithi
2022-03-03Run partial correlations in an external process...Run the partial correlations code in an external python process decoupling it from the server and making it asynchronous. Summary of changes: * gn3/api/correlation.py: - Remove response processing code - Queue partial corrs processing - Create new endpoint to get results * gn3/commands.py - Compose the pcorrs command to be run in an external process - Enable running of subprocess commands with list args * gn3/responses/__init__.py: new module indicator file * gn3/responses/pcorrs_responses.py: Hold response processing code extracted from ~gn3.api.correlations.py~ file * scripts/partial_correlations.py: CLI script to process the pcorrs * sheepdog/worker.py: - Add the *genenetwork3* path at the beginning of the ~sys.path~ list to override any GN3 in the site-packages - Add any environment variables to be set for the command to be run Frederick Muriuki Muriithi
2022-02-11Quote shell variables to prevent globbing...Quote the shell variables to prevent globbing and word splitting. Deactivate this check for the specific lines that require intentional word splitting Frederick Muriuki Muriithi
2022-02-02Fix R/qtl covar bug...The rqtl_wrapper script was throwing an error when only a single categorical covariate was used. This is apparently because "covars[,name]" throws an error in such a situation. Using just "covars" in such a situation prevents the error. So I just added an if statement checking the number of covariates. There might be some better way to deal with this in R, but this is the best I could come up with. zsloan
2022-02-02remove commentsAlexander Kabui
2022-02-02match case string input to booleanAlexander Kabui
2022-02-02fix for parametric inputAlexander Kabui
2022-02-02use user input significanceAlexander Kabui
2022-02-02new line fixAlexander Kabui
2022-02-02add new json outputAlexander Kabui
2022-01-22minor refactoringAlexander Kabui
2022-01-22function override:fix target specific output file for networkAlexander Kabui
2022-01-22generate networkAlexander Kabui
2022-01-22generate ctl plots for each traitAlexander Kabui
2022-01-22fixes for ctl script:generate ctl ctl_significant jsonAlexander Kabui
2022-01-22bugfixes for script;create pheno and geno objectsAlexander Kabui
2022-01-22generate lineplotAlexander Kabui
2022-01-22minor fix:read input data from json fileAlexander Kabui
2022-01-22export json dataAlexander Kabui
2022-01-22get significant interactionsAlexander Kabui
2022-01-22perform the ctl scanAlexander Kabui
2022-01-22fetch genotypes and phenotype filesAlexander Kabui
2022-01-22init script ctl analysisAlexander Kabui
2021-12-22Refactor wgcna (#63)...* add r as a gn3 input * calculate powers from user input * fix merge conflictAlexander Kabui
2021-11-11Merge branch 'main' into feature/add_rqtl_pairscanzsloan
2021-10-29Feature/biweight reimplementation (#47)...* add biweight reimplementation with pingouin * delete biweight scripts and tests * add python-pingouin to guix file * delete biweight paths * mypy fix:pingouin mising imports * pep8 formatting && pylint fixesAlexander Kabui
2021-10-25minor fixes for sript enable annotationsAlexander Kabui
2021-10-25script modification : add debug statementsAlexander Kabui
2021-10-14Fixed when model is set to account for situations with no covariateszsloan
2021-10-14Incorporated Danny's code for calculating QTL main effects into rqtl_wrapper.Rzsloan
2021-10-12Merge branch 'main' of https://github.com/genenetwork/genenetwork3 into bug/f...zsloan
2021-10-12Merge branch 'main' of https://github.com/genenetwork/genenetwork3 into featu...zsloan
2021-09-27remove unnecessary comments and variablesAlexander Kabui
2021-09-23Updated rqtl_wrapper to also return a map file when doing a pair-scan (since ...zsloan
2021-09-23Added line priting pair-scan results to CSV and changed the default step-size...zsloan
2021-09-23- Added scan_func function that determines whether scanone or scantwo...(pairscan) is used - For pairscan default to using step 20 (subject to change, but some step is required during calc.genoprob to make it run fast enough) - Added some new verbose prints zsloan
2021-09-23Added option for running pairscan to rqtl_wrapper.Rzsloan
2021-09-23Fix covariates as described by Dannyzsloan