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AgeCommit message (Expand)Author
2022-06-29add test dataAlexander
2022-06-29parse output dataAlexander
2022-06-29init test correlation rust moduleAlexander
2022-05-30Pass trait data as args to `fix_strains` and fix some bugs...The `fix_strains` function works on the trait data, not the basic trait info. This commit fixes the arguments passed to the function, and also some bugs in the function. Frederick Muriuki Muriithi
2022-03-15Feature/refactored pca (#79)...* compute zscore function * test case for computing zscore * function to compute pca * generate scree plot data * generate new pca trait data from zscores and eigen_vec * remove redundant functions * generate factor loading table data * generate pca temp dataset dict * variable naming and error fixes * unit test for processing factor loadings * minor fixes for generating temp pca dataset * pass datetime as argument to generate_pca temp dataset function * add unittest for caching pca datasets * cache temp datasets * ignore missing imports for sklearn * mypy fixes * pylint fixes * refactor tests for pca * remove ununsed imports * fix for generating pca traits vals * mypy and code refactoring * pep8 formatting and add docstrings * remove comments /pep8 formatting * sort eigen vectors based on eigen values * minor fix for zscores * fix for rounding variance ratios * refactor tests * rename module to pca * rename datasets to traits * fix failing tests * fix caching function * fixes return x and y coordinates for scree plot * expand exception scope * fix for deprecated numpy.matrix function * fix for failing tests * pep8 fixes * remove comments * fix merge conflict * pylint fixes * rename module name to test_pcaAlexander Kabui
2022-03-08Remove unused function and its testsFrederick Muriuki Muriithi
2022-02-24gn3: Explicitly specify UTF-8 to be the file encoding....When the encoding is not specified explicitly, the system default encoding is used. This is not recommended. * gn3/computations/ctl.py (call_ctl_script), gn3/computations/gemma.py (generate_pheno_txt_file), gn3/computations/parsers.py (parse_genofile), gn3/computations/partial_correlations.py (partial_correlations_fast), gn3/computations/rqtl.py (process_rqtl_output, process_perm_output), gn3/computations/wgcna.py (dump_wgcna_data, call_wgcna_script), gn3/fs_helpers.py (jsonfile_to_dict): Explicitly specify UTF-8 to be the file encoding. * tests/unit/computations/test_gemma.py (TestGemma.test_generate_pheno_txt_file), tests/unit/computations/test_wgcna.py (TestWgcna.test_create_json_file): Test for call to open with encoding='utf-8' argument. Arun Isaac
2022-02-21Fix a myriad of linter issues...* Use `with` in place of plain `open` * Use f-strings in place of `str.format()` * Remove string interpolation from queries - provide data as query parameters * other minor fixes Frederick Muriuki Muriithi
2022-02-17Use pytest's "mark" feature to categorise tests...Use pytest's `mark` feature to explicitly categorise the tests and run them per category Frederick Muriuki Muriithi
2022-02-17Add property tests for `dictify_by_samples`...Add property tests using pytest and hypothesis to test that the expected properties hold for the `gn3.computations.partial_correlations.dictify_by_samples` function. Frederick Muriuki Muriithi
2021-12-14linting: Fix obvious linting issuesFrederick Muriuki Muriithi
2021-12-10refactor sample r unittestsAlexander Kabui
2021-12-10refactor unittest for normalizing sample valuesAlexander Kabui
2021-11-29Update test for data changes...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi Frederick Muriuki Muriithi
2021-11-19Avoid rounding: compare floats approximately...Notes: https://github.com/genenetwork/genenetwork3/pull/56#issuecomment-973798918 * As mentioned in the notes, rather than rounding to an arbitrary number of decimal places, it is a much better practice to use approximate comparisons of floats for the tests. Frederick Muriuki Muriithi
2021-11-18Fix some linting errors...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Fix some obvious linting errors and remove obsolete code Frederick Muriuki Muriithi
2021-11-18Replace code migrated from R with pingouin functions...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Replace the code that was in the process of being migrated from R in GeneNetwork1 with calls to pingouin functions that achieve the same thing. Since the functions in this case are computing correlations and partial correlations, rather than having home-rolled functions to do that, this commit makes use of the tried and tested pingouin functions. This avoids complicating our code with edge-case checks, and leverages the performance optimisations done in pingouin. Frederick Muriuki Muriithi
2021-11-15Fix bugs in recursive partial correlations...* gn3/computations/partial_correlations.py: Remove rounding. Fix computation of remaining covariates * tests/unit/computations/partial_correlations_test_data/pcor_rec_blackbox_test.txt: reduce the number of covariates to between one (1) and three (3) * tests/unit/computations/test_partial_correlations.py: fix some minor bugs It turns out that the computation complexity increases exponentially, with the number of covariates. Therefore, to get a somewhat sensible test time, while retaining a large-ish number of tests, this commit reduces the number of covariates to between 1 and 3. Frederick Muriuki Muriithi
2021-11-15Fix the columns in built data frame...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * When the z value is a Sequence of sequences of values, each of the internal sequences should form a column of its own, and not a row, as it was originally set up to do. Frederick Muriuki Muriithi
2021-11-12Merge branch 'main' of github.com:genenetwork/genenetwork3 into partial-corre...Frederick Muriuki Muriithi
2021-11-12Pass in parser function for flexibility...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * To improve the usefulness of already existing code, provide the parser function as an argument to the `parse_input_line` function. This was found to be useful when writing code to compare the `pcor.test` function in GN1 and the `pingouin.partial_corr` function. The format of the data generated when getting results for the `pcor.test` function shared a lot with that of the `pcor.rec` function, but it was different in a few, places, and the differences were non-trivial, needing different parsing processes. In such a case, it was found necessary to just pass in the function to do the actual parsing, rather than create code with the same form as the existing one, save for the function being called. Frederick Muriuki Muriithi
2021-11-11Reimplement correlations2.compute_correlation using pearsonr....correlations2.compute_correlation computes the Pearson correlation coefficient. Outsource this computation to scipy.stats.pearsonr. When the inputs are constant, the Pearson correlation coefficient does not exist and is represented by NaN. Update the tests to reflect this. * gn3/computations/correlations2.py: Remove import of sqrt from math. (compute_correlation): Reimplement using scipy.stats.pearsonr. * tests/unit/computations/test_correlation.py: Import math. (TestCorrelation.test_compute_correlation): When inputs are constant, set expected correlation coefficient to NaN. Arun Isaac
2021-11-11Compare floats approximately....Floating point numbers should only be compared approximately. Different implementations of functions might produce slightly different results. * tests/unit/computations/test_correlation.py: Import assert_almost_equal from numpy.testing. (TestCorrelation.test_compute_correlation): Compare floats using assert_almost_equal instead of assertEqual. * tests/unit/test_heatmaps.py: Import assert_allclose from numpy.testing. (TestHeatmap.test_cluster_traits): Use assert_allclose instead of assertEqual. Arun Isaac
2021-11-11pep8 formatting;update unittestsAlexander Kabui
2021-11-09Merge branch 'main' of github.com:genenetwork/genenetwork3 into partial-corre...Frederick Muriuki Muriithi
2021-11-09Implement remaining part of `partial_correlation_recursive` function...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/computations/partial_correlations.py: implement remaining portion of `partial_correlation_recursive` function. * tests/unit/computations/test_partial_correlations.py: add parsing for new data format and update tests Frederick Muriuki Muriithi
2021-11-09Update test data: have both vectors and matrices...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Delete the older test data that was only testing with `z` being a vector and replace it with data that has `z` being a vector or matrix from data item to data item. Frederick Muriuki Muriithi
2021-11-04test_partial_correlations: skip failing tests...Fix these later. I need a passing test suite so as to update the gn2 docker image. BonfaceKilz
2021-11-04Create blackbox tests for some functions migrated from R...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. Frederick Muriuki Muriithi
2021-11-04Retrieve indices of the selected samples...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. Frederick Muriuki Muriithi
2021-11-04Specify ten (10) decimal places...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. Frederick Muriuki Muriithi
2021-11-04Fix some linting errors...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi Frederick Muriuki Muriithi
2021-11-04Implement `tissue_correlation` function...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. Frederick Muriuki Muriithi
2021-11-04Partially implement `partial_correlation_recursive`...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/computations/partial_correlations.py: Implement one path for the `gn3.computations.partial_correlations.partial_correlation_recursive` function. * gn3/settings.py: Add a setting for how many decimal places to round to * tests/unit/computations/test_partial_correlations.py: Update test to take the number of decimal places into consideration Implement a single path (where the z value is a vector and not a matrix) for the `partial_correlation_recursive` function. Frederick Muriuki Muriithi
2021-11-04Implement `build_data_frame`...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 (`build_data_frame`) * tests/unit/computations/test_partial_correlations.py: Add tests for new function Add a new function to build a pandas DataFrame object from the provided values: - x: a vector of floats (represented with a tuple of floats) - y: a vector of floats (represented with a tuple of floats) - z: a vector OR matrix of floats (represented with a tuple of floats or a tuple of tuples of floats) Frederick Muriuki Muriithi
2021-11-04Create blackbox tests for some functions migrated from R...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. Frederick Muriuki Muriithi
2021-11-01Merge branch 'main' of github.com:genenetwork/genenetwork3 into partial-corre...Frederick Muriuki Muriithi
2021-11-01Retrieve indices of the selected samples...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. Frederick Muriuki Muriithi
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
2021-10-29Specify ten (10) decimal places...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. Frederick Muriuki Muriithi
2021-10-29Fix some linting errors...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi Frederick Muriuki Muriithi
2021-10-29Implement `tissue_correlation` function...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. Frederick Muriuki Muriithi
2021-10-25fix unittestsAlexander Kabui
2021-09-27modify unittestsAlexander Kabui
2021-09-27add tests for calling wgcna_scriptAlexander Kabui
2021-09-27fix merge conflictsAlexander Kabui
2021-09-27Update terminology: `strain` to `sample`...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 Frederick Muriuki Muriithi
2021-09-25minor fixes for unittestsAlexander Kabui
2021-09-23Refactor: Move common sample data to separate file...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Move common sample test data into a separate file where it can be imported from, to prevent pylint error R0801 which proved tricky to silence in any other way. Frederick Muriuki Muriithi
2021-09-22add init tests for call to scriptAlexander Kabui