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2021-06-18fix index error (#16)Alexander Kabui
2021-05-25Include code that processes rqtl output files and returns actual results ↵zsloan
instead of just the output filename
2021-05-19Temporarily replace forward-slashes with underscores, since they can be ↵zsloan
included in the hashes used for filenames
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)
2021-05-18Fixed 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
2021-05-15resolve merge conflictAlexander Kabui
2021-05-15Merge branch 'main' into feature/minor-fixesAlexander Kabui
2021-05-15index lit tuple resultAlexander Kabui
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
2021-05-08Add extra procedure for parsing a genotype fileBonfaceKilz
* gn3/computations/parsers.py (parse_genofile): New procedure. * tests/unit/computations/test_parsers.py: New test files for above.
2021-05-03add default no of coresAlexander Kabui
2021-05-03add trait_id fix mypy issuesAlexander Kabui
2021-05-03minor fixes for tiss correlation tests and namingAlexander Kabui
2021-05-03replace database with connAlexander Kabui
2021-05-02delete dataset and trait filesAlexander Kabui
2021-04-20pep8 formattingAlexander Kabui
2021-04-20add experiment function for computing tissue correlation using multiprocessingAlexander Kabui
2021-04-18refactor:return trait_name in corr_resultsAlexander Kabui
2021-04-17ad pep8 formattingAlexander Kabui
2021-04-17add sort for correlation resultsAlexander Kabui
refactor return data type for tissue and lit
2021-04-16add benchmark function for sample rAlexander Kabui
2021-04-16benchmark normal function for sample rAlexander Kabui
2021-04-15optimization for sample correlationAlexander Kabui
2021-04-15test endpoint for fetching probeset data typesAlexander Kabui
2021-04-12fix merge conflictAlexander Kabui
2021-04-12Integrate correlation APIAlexander Kabui
- add new api for gn2-gn3 sample r integration - delete map for sample list to values - add db util file - add python msql-client dependency - add db for fetching lit correlation results - add unittests for db utils - add tests for db_utils - modify api for fetching lit correlation results - refactor Mock Database Connector and unittests - add sql url parser - add SQL URI env variable - refactor code for db utils - modify return data for lit correlation - refactor tissue correlation endpoint - replace db_instance with conn
2021-04-06fix DocstringsAlexander Kabui
2021-04-06delete unnecessary functions and commentsAlexander Kabui
2021-04-05fix for fetching dataset traits dataAlexander Kabui
2021-04-04refactor code for trait dataAlexander Kabui
modify unittest and integration tests for datasets
2021-04-03add tests for getting trait dataAlexander Kabui
2021-03-31add mysqlclient in guixAlexander Kabui
add env variable for GN2_URL
2021-03-31add datasets functions and endpointsAlexander Kabui
2021-03-30refactor retrieve trait sample data and testsAlexander Kabui
2021-03-30modify getting sample data from dbAlexander Kabui
2021-03-30initial commit for creating datasetAlexander Kabui
2021-03-30initial commit for creating trait and datasetsAlexander Kabui
2021-03-23Re-add mypy conf fileBonfaceKilz
Deleted in 56ce88a
2021-03-17gn3: computations: correlations: Apply autopep-8.BonfaceKilz
2021-03-16Refactor/clean up correlations (#4)Alexander Kabui
* initial commit for Refactor/clean-up-correlation * add python scipy dependency * initial commit for sample correlation * initial commit for sample correlation endpoint * initial commit for integration and unittest * initial commit for registering correlation blueprint * add and modify unittest and integration tests for correlation * Add compute compute_all_sample_corr method for correlation * add scipy to requirement txt file * add tissue correlation for trait list * add unittest for tissue correlation * add lit correlation for trait list * add unittests for lit correlation for trait list * modify lit correlarion for trait list * add unittests for lit correlation for trait list * add correlation metho in dynamic url * add file format for expected structure input while doing sample correlation * modify input data structure -> add trait id * update tests for sample r correlation * add compute all lit correlation method * add endpoint for computing lit_corr * add unit and integration tests for computing lit corr * add /api/correlation/tissue_corr/{corr_method} endpoint for tissue correlation * add unittest and integration tests for tissue correlation Co-authored-by: BonfaceKilz <bonfacemunyoki@gmail.com>
2021-03-10Fix k-compute command when "loco" is trueBonfaceKilz
2021-03-08Remove unused importsBonfaceKilz
2021-03-08Delete "generate_gemma_computation_cmd"BonfaceKilz
2021-03-08Add generic fn for computing k and gwa valuesBonfaceKilz
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