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2021-06-18db: phenotype: Make "pylint: disable=[R0902]" global for fileBonfaceKilz
2021-06-18tests: test_phenotypes: New test cases for loading phenotypesBonfaceKilz
2021-06-18db: phenotypes: Add a way of updating the Phenotype tableBonfaceKilz
* gn3/db/phenotypes.py (Phenotype): New dataclass. (update_phenotype): New function. [phenotype_column_mapping]: New variable.
2021-06-18Fixed issue where all bool kwargs were always being passed to ↵zsloan
generate_rqtl_cmd and also made code check if output file already exists (so caching works)
2021-06-18Added option for enabling permutation stratazsloan
Fixed issue where covariates with numerical names were being ignored Fixed issue where the hash filename wasn't being used for the permutation output
2021-06-18Add rqtl_wrapper.R script and necessary imports to guix.scmzsloan
2021-06-18Fix R/qtl command and the way keyword arguments are passedzsloan
2021-05-25Include code that processes rqtl output files and returns actual results ↵zsloan
instead of just the output filename
2021-05-19Merge branch 'main' of https://github.com/genenetwork/genenetwork3 into ↵zsloan
feature/add_rqtl_endpoints
2021-05-19Add r-optparse to guix.scmPjotr Prins
2021-05-19Temporarily replace forward-slashes with underscores, since they can be ↵zsloan
included in the hashes used for filenames
2021-05-19Merge branch 'main' of https://github.com/genenetwork/genenetwork3 into ↵zsloan
feature/add_rqtl_endpoints
2021-05-19Added R and r-qtlPjotr Prins
2021-05-19More SQL optimization trialsPjotr Prins
2021-05-19Fix SQL queryPjotr Prins
2021-05-19SQL query gives different resultPjotr Prins
2021-05-19New SQL approachPjotr Prins
2021-05-18Added test for compose_rqtl_cmd in tests/unit/test_commands.pyzsloan
2021-05-18Removed len from this if statement, since an empty list evaluates to False ↵zsloan
by itself
2021-05-18Added unit test for computations/rqtl.pyzsloan
2021-05-18Account for boolean kwargs in compute() by storing them in a list, since ↵zsloan
they don't have corresponding values
2021-05-18Account for boolean kwargs in compose_rqtl_cmdzsloan
2021-05-18Fixed 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)
2021-05-18Slow SQL: add notePjotr Prins
2021-05-18Add original SQL queryPjotr Prins
2021-05-18Notes on SQL queryPjotr Prins
2021-05-18Fixed variety of issues detected by pylintzsloan
2021-05-17Created 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
2021-05-17Read in kwargs fromrequest and pass the command, tmpdir, and kwargs to ↵zsloan
generate_rqtl_cmd which returns the actual command and output path
2021-05-17Added RQTL_WRAPPER_CMD (which is fetched from environment) in settings.pyzsloan
2021-05-17Add rqtl.py for rqtl endpointszsloan
2021-05-17Register rqtl blueprintzsloan
2021-05-17Merge pull request #11 from genenetwork/feature/minor-fixesBonfaceKilz
Feature/minor fixes
2021-05-15resolve merge conflictAlexander Kabui
2021-05-15Merge branch 'main' into feature/minor-fixesAlexander Kabui
2021-05-15index lit tuple resultAlexander Kabui
2021-05-14READMEPjotr Prins
2021-05-13tests: test_general: Add test case for run_r_qtl endpointBonfaceKilz
2021-05-13Add end-point for running an rQTL programBonfaceKilz
* gn3/api/general.py (run_r_qtl): New function. * gn3/settings.py: New variable.
2021-05-13Rename file_utils to fs_helpersBonfaceKilz
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...
2021-05-13computations: correlations: Apply pep-8BonfaceKilz
2021-05-12delete unused functionsAlexander Kabui
2021-05-12rename lit_correlation_for_trait_list to lit_correlation_for_traitAlexander Kabui
2021-05-12rename tissue_correlation_for_trait_list with tissue_correlation_for_traitAlexander Kabui
2021-05-12rename p_val ro tissue_p_value for tissue_resultsAlexander Kabui
2021-05-10tests: test_species: Add test for `get_all_species`BonfaceKilz
2021-05-10db: species: Add method for fetching all speciesBonfaceKilz
2021-05-10tests: test_gemma: Add TMPDIR to test_client()BonfaceKilz
2021-05-10setup.py: Add gn3.api to packagesBonfaceKilz
2021-05-10setup.py: Remove gn3.utility from packagesBonfaceKilz
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