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2021-08-20Minor correlation fixes (#36)Alexander Kabui
* fix key error for (*tissue_cor) tissue correlation * update tests for tissue correlation * rename speed_compute to fast_compute * pep8 formatting
2021-08-18Test the clusteringMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/heatmap.py: Fix clustering bugs * tests/unit/computations/test_heatmap.py: Add new tests. Fix linting issues. Test and fix the clustering function.
2021-08-18Add tests and fix errors caught with testsMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/heatmap.py: fix errors * tests/unit/computations/test_heatmap.py: new tests Add new tests with the expected source data format, and expected results. Fix all errors that were caught by running the tests
2021-08-11use normal function for correlation (#34)Alexander Kabui
* use normal function for correlation + rename functions * update test for sample correlation * use normal function for tissue correlation + rename functions
2021-07-26Fix issues caught by pylintMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Fix a myriad of issues caught by pylint to ensure the code passes all tests.
2021-07-23Add data examples for `slink`. Implement function.Muriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/slink.py: Copy the function, mostly verbatim from genenetwork1. See: https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py#L107-L138 * tests/unit/computations/test_slink.py: Add a test with some example data to test that the implementation gives the same results as that in genenetwork1
2021-07-23Add more test dataMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
2021-07-23Fix issue caught in `nearest` while testing `slink`Muriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * While running tests for slink, to try and understand what it is doing in order to write the appropriate tests for it, an issue arose that pointed a blindspot in the former understanding of now `nearest` should work. This commit fixes the issue found in both the expected data, and the code.
2021-07-23New function (`slink`): return [] on exceptionMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/slink.py: Add minimum code to pass new test * tests/unit/computations/test_slink.py: new test Add test to ensure that the new `slink` function return an empty list in case and exception is raised. Add the new `slink` function with minimum amount of code needed to pass the test.
2021-07-22Get shortest distance from two lists/tuples of member coordinatesMuriithi Frederick Muriuki
* gn3/computations/slink.py: add code to ensure new test passes * tests/unit/computations/test_slink.py: new test This one is a little weird: from https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py#L57-L63 It gets rid of the last coordinates in both the lists of the member coordinates, and uses the remaining coordinates to find the shortest members. For example, given the following member coordinates: - i=[0,1,2] and j=[5,7,9], it uses [0,1] and [5,7] - i=[3,6,1] and j=[7,13], it uses [3,6] and [7] to find the shortest distances. I (fredmanglis) am not sure why it does it this way, since I'd have expected it to use all the coordinates, however, since at this time we need to retain bug-compatibility with the older code, I have done it as it is done in the old code. I also add a statement to raise an exception in the case where i and j are not lists of integers, or integers
2021-07-22Test for shortest distance between members in a list and coordinateMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/slink.py: add code to pass new test * tests/unit/computations/test_slink.py: new test Given a list of members in a group, and a coordinate for a member in the same group, find the distance of the closest member from the given coordinate in the group.
2021-07-22Check that given list and both coordinates, we get shortest distanceMuriithi Frederick Muriuki
* gn3/computations/slink.py: Add code to compute the distance given the coordinate of both members on the parent list/tuple * tests/unit/computations/test_slink.py: * Change the name of the tests to more closely correspond to the business requirement the test is checking for * Update the comments to indicate some more things that might need to be done in the future
2021-07-22Check that all distances are positive or zeroMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/slink.py: check that all distances between the 'somethings' are all either zero or positive. * tests/unit/computations/test_slink.py: * Remove data with all distances positive or zero, since it would fail the test * Change the expected message to more closely correspond to the business logic
2021-07-22Check that distance from A to B is same as from B to AMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/slink.py: check that the distance from child A to B is the same as distance from child B to A. If not, throw an exception. * tests/unit/computations/test_slink.py: * Change the name of the test to more closely correspond to the business logic being tested. * Update the data in a separate test such that it does not error out due to failing to fulfill the expectations of separate requirement. - pass tests - Rename test - Fix errors: distances same both directions
2021-07-22Check that child distance from itself is zeroMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/slink.py: Check that a child's distance from itself is zero. If not, throw an exception. The children lists are a list of distances of "something" from other "somethings". There is still some need to establish what those "somethings" are, so that the test names can reflect the ideas that are actually being tested for. * tests/unit/computations/test_slink.py: Change the name of the test so that it more closely corresponds to the business logic it is actually testing, and not the mechanics of testing the idea.
2021-07-21Extract tests from code in GN1Muriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/slink.py: Add dummy `nearest' function * tests/unit/computations/test_slink.py: Add some tests This commit adds tests to try and reproduce the working of the `nearest' function in: https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py This commit might not yet have extracted all the expected behaviour of the `nearest' function, and therefore, there is a possibility of a later commit augmenting the work in this commit.
2021-07-20Add test for code to move over from GN1Muriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * .gitignore: ignore emacs temporary files * gn3/computations/correlations2.py: add a dummy function * tests/unit/computations/test_correlation.py: add unit tests for the function As part of the move of the clustering and heatmap code over from GN1 to GN3, this commit begins by providing some unit tests for the correlation function used to ensure that the implementation that is built up here corresponds, and produces the same results as the original. This tests and the function might change in the new system, but for now, we try and maintain bug-to-bug compatibility.
2021-06-29Add a diffing functionBonfaceKilz
For now the diff function uses the Linux tool "diff" to generate the diff since it is efficient and straightforward. * gn3/computations/diff.py (generate_diff): New function. * tests/unit/computations/test_diff.py: Test cases for ☝🏾.
2021-06-20merge mainAlexander Kabui
2021-06-20make requested changes to biweightAlexander Kabui
2021-06-18Fixed another error where test_generate_rqtl_command didn't include the ↵zsloan
filename argument (not sure why running unit tests locally doesn't detect this)
2021-06-18Fixed file type from json to csv for test_generate_rqtl_commandzsloan
2021-06-18Fixed test_rqtl.py to include Rscript in the commandzsloan
2021-06-18fix index error (#16)Alexander Kabui
2021-06-14add biweight r script and testsAlexander Kabui
2021-05-30fix index error (#16)Alexander Kabui
2021-05-18Added unit test for computations/rqtl.pyzsloan
2021-05-15index lit tuple resultAlexander Kabui
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
2021-05-08Fix typoBonfaceKilz
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.
2021-05-03minor fixes for tiss correlation tests and namingAlexander Kabui
2021-05-03replace database with connAlexander Kabui
2021-05-02delete dataset and trait filesAlexander Kabui
2021-04-18refactor:return trait_name in corr_resultsAlexander Kabui
2021-04-17ad pep8 formattingAlexander Kabui
2021-04-17refactor tests for litAlexander Kabui
2021-04-15optimization for sample correlationAlexander Kabui
2021-04-12fix tests for lit correlationAlexander 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 fetch dataset strain id,strain name and unittestsAlexander Kabui
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