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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
2021-07-22Extract common `is_list_or_tuple' functionMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Extract the common function `is_list_or_tuple' making it accessible to later parts of the code.
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.
2021-07-22Check the child lengths are same as length of parentMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Check that the child lists/tuples are the same length as the parent list/tuple. If any of the children is not the same length as the parent, throw and exception.
2021-07-22Add docstringMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Add docstring to the function, useful for generating automated developer documentation. We also surround the guard functions with some notification comments, to mark possible future places where change might be done.
2021-07-22Check that list and its direct children are not emptyMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Add code to pass the test that the list/tuple passed to `nearest' and its direct children lists/tuples are not empty.
2021-07-22Implement check for lists or tuplesMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Implement the code to pass the check that a list of lists is passed to the `nearest' function.
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.
2021-07-20Implement the correlation functionMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Implement the correlation computation function, such that it passes the tests created previously.
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.
2021-06-29Replace list with a tuple as an argument when setting success_codesBonfaceKilz
* gn3/commands.py (run_cmd): Replace type of success_codes from List to Tuple * gn3/computations/diff.py (generate_diff): Pass success_codes as a Tuple when calling "run_cmd".
2021-06-29gn3: diff: Set success_codes when running the diff toolBonfaceKilz
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 ☝🏾.
2021-06-23fix pylint issuesAlexander Kabui
2021-06-23minor fixes for biweight scriptAlexander Kabui
2021-06-20minor fix docstringAlexander Kabui
2021-06-20merge mainAlexander Kabui
2021-06-20make requested changes to biweightAlexander Kabui
2021-06-18Fixed pylint issueszsloan
2021-06-18Resolve mypy errors in computations/rqtl.pyzsloan
2021-06-18Fixed spelling of coeffient to coefficientzsloan
2021-06-18fix index error (#16)Alexander Kabui
2021-06-16add r-wgna packageAlexander Kabui
2021-06-16minor fixAlexander Kabui
2021-06-16refactor script and add testsAlexander Kabui
2021-06-16add fetch args functionAlexander Kabui
2021-06-15fix script path issuesAlexander Kabui
2021-06-14fix missing call to bicorAndPvalueAlexander Kabui
2021-06-14add biweight r script and testsAlexander Kabui
2021-05-30fix 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
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