aboutsummaryrefslogtreecommitdiff
path: root/gn3/computations
AgeCommit message (Collapse)Author
2021-11-11Merge branch 'main' into feature/add_rqtl_pairscanzsloan
2021-11-11pylint fixes and pep8 formattingAlexander Kabui
2021-11-11fix target and base sample data orderAlexander Kabui
2021-11-11fix:spawned processes memory issuesAlexander Kabui
2021-11-11replace list with generatorsAlexander Kabui
2021-11-04Create blackbox tests for some functions migrated from RFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/computations/partial_correlations.py: new stub functions (partial_correlation_matrix, partial_correlation_recursive) * tests/unit/computations/partial_correlations_test_data/pcor_mat_blackbox_test.csv: blackbox sample data and results for variance-covariance matrix method * tests/unit/computations/partial_correlations_test_data/pcor_rec_blackbox_test.csv: blackbox sample data and results for recursive method * tests/unit/computations/test_partial_correlations.py: Tests for new function Provide some blackbox testing sample data for checking the operation of the functions migrated from R.
2021-11-04Stub `determine_partials`Frederick Muriuki Muriithi
Issue: * Stub out `determine_partials` which is a migration of `web.webqtl.correlation.correlationFunction.determinePartialsByR` in GN1. The function in GN1 has R code from line 188 to line 344. This will need to be converted over to Python. This function will also need tests.
2021-11-04Implement `compute_partial_correlations_fast`Frederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Implement `compute_partial_correlations_fast` that is a partial migration of `web.webqtl.correlation.PartialCorrDBPage.getPartialCorrelationsFast` in GN1. This function will probably be reworked once the dependencies are fully migrated. It also needs tests to be added.
2021-11-04Retrieve indices of the selected samplesFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/computations/partial_correlations.py: New function (good_dataset_samples_indexes). * tests/unit/computations/test_partial_correlations.py: Tests for new function (good_dataset_samples_indexes) Get the indices of the selected samples. This is a partial migration of the `web.webqtl.correlation.PartialCorrDBPage.getPartialCorrelationsFast` function in GN1.
2021-11-04Explicitly round the valuesFrederick Muriuki Muriithi
* Explicitly round the values to prevent issues with the type-checker
2021-11-04Specify ten (10) decimal placesFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/computations/partial_correlations.py: specify 10 decimal places * tests/unit/computations/test_partial_correlations.py: update examples Slight differences in python implementations, possibly hardware and operating systems could cause the value of float (double) values to be different in the less significant parts of the decimal places. This commit limits the usable part of the decimals to the first 10 decimal places for now.
2021-11-04Fix linting and typing errorsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
2021-11-04Complete `build_temporary_tissue_correlations_table`Frederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/computations/partial_correlations.py: Remove comments after updating usage of the function at call point * gn3/db/correlations.py: Complete the implementation of the `build_temporary_tissue_correlations_table` function
2021-11-04Complete implementation of `batch_computed_tissue_correlation`Frederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Complete the implementation of the `batch_computed_tissue_correlation` function
2021-11-04Move `correlations_of_all_tissue_traits`Frederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/computations/partial_correlations.py: new function (`correlations_of_all_tissue_traits`). * gn3/db/correlations.py: delete function (`correlations_of_all_tissue_traits`). Move the function to `gn3.computations.partial_correlations` module and comment out the db-access code. Rework it to receive, as arguments, the data it previously fetched from the database, and add comments on future rework to get the function working again.
2021-11-04Implement `tissue_correlation` functionFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/computations/partial_correlations.py: New function (tissue_correlation) * tests/unit/test_partial_correlations.py -> tests/unit/computations/test_partial_correlations.py: Move module. Implement tests for new function Migrate the `cal_tissue_corr` function embedded in the `web.webqtl.correlation.correlationFunction.batchCalTissueCorr` function in GN1 and implement tests to ensure it works correctly.
2021-11-04Move the function to computations moduleFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * The function `batch_computed_tissue_correlation` is a pure computations function with no expressions accessing the database, as far as I can tell, therefore, this commit moves the function over to the gn3.computations.partial_correlations module that holds the pure computation functions.
2021-11-04Move the partial_correlations module to gn3.computationsFrederick Muriuki Muriithi
* Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Move the partial_correlations.py module to the gn3.computations module, since it contains the computations for partial correlations.
2021-10-29Feature/biweight reimplementation (#47)Alexander Kabui
* 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 fixes
2021-10-25mypy:Incompatible types in assignment fixAlexander Kabui
2021-10-25mypy fix for none stdoutAlexander Kabui
2021-10-25pylint and pep8 formattingAlexander Kabui
2021-10-25fix unittestsAlexander Kabui
2021-10-25minor modification for emitting data:add namespacesAlexander Kabui
2021-10-25pep8 formatting,pylint fixesAlexander Kabui
2021-10-25add socket obj and emit processAlexander Kabui
2021-10-25fix issues serializing byte stringAlexander Kabui
2021-10-25rename key to image_dataAlexander Kabui
2021-10-25add function to process imagesAlexander Kabui
2021-10-25add function to capture output in real timeAlexander Kabui
2021-10-12Fixes pylint errorszsloan
2021-10-12Fixed mypy typing errorszsloan
2021-10-12Merge branch 'main' of https://github.com/genenetwork/genenetwork3 into ↵zsloan
feature/add_rqtl_pairscan
2021-09-27add file not found exceptionAlexander Kabui
2021-09-27return str error for exceptionAlexander Kabui
2021-09-27fix merge conflictsAlexander Kabui
2021-09-27Narrow the exception and add commentsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Only catch the `FileExistsError` allowing any other exception to pass through. This tries to conform a little to the review at https://github.com/genenetwork/genenetwork3/pull/37#discussion_r714552696
2021-09-27Update terminology: `strain` to `sample`Frederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Update the terminology used: use `sample` in place of `strain` according to Zachary's direction at https://github.com/genenetwork/genenetwork3/pull/37#issuecomment-926043306
2021-09-23Tried to make the docstrings more consistentzsloan
2021-09-23Merge branch 'feature/add_rqtl_pairscan' of ↵zsloan
https://github.com/zsloan/genenetwork3 into feature/add_rqtl_pairscan
2021-09-23Add typing to some functionszsloan
2021-09-23Add functions for getting proximal/distal markers for each pseudomarker ↵zsloan
position in pair-scan results + return only the sorted top 500 results
2021-09-23Added 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
2021-09-23Removed quotes from beginning and end of chromosome stringzsloan
2021-09-23Fixed a cople function calls to use the updated function nameszsloan
2021-09-23Create 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
2021-09-23Added 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
2021-09-23minor fixes for endpointAlexander Kabui
2021-09-23Return r error if returncode!=0Alexander Kabui
2021-09-23read generated files from r and return outputAlexander Kabui
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 11:06:01 +0000