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2021-09-08Ease search for traits and chromosomesMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Return a dict of values rather than list for the traits and chromosomes to ease searching through the data.
2021-09-08Parse Chr value as int where possibleMuriithi Frederick Muriuki
* To ease sorting of data by numerical order down the line, sort the "Chr" values by numerical order.
2021-09-08Remove extraneous text to ease sortingMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Change the id from 'T<n>' to simply '<n>' to ease sorting of the trait results by numerical order rather than string order.
2021-09-08Fix the traits order computations for 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 ordering function * tests/unit/computations/test_heatmap.py: update test The order of the traits is important for the clustering algorithm, since the clustering seems to use the distance of one trait from another to determine how to order them. This commit also gets rid of the xoffset argument that is not important to the ordering, and was used in the older GN1 to determine how to draw the clustering lines.
2021-09-06Provide function to organise parsed QTLReaper resultsMuriithi Frederick Muriuki
* gn3/computations/qtlreaper.py: Provide a function to organise the results by trait for easier use down the line. * tests/unit/computations/test_qtlreaper.py: provide a test to ensure that the organising function works as expected.
2021-09-06Leave "Chr" value as string when parsingMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * The "Chr" value seems to be mostly a name of some sort, despite it being, seemingly an number. This commit parses the "Chr" value as a string. It also updates the tests to expec a string, rather than a number for "Chr" values.
2021-09-06Handle type-coercion exceptionsMuriithi Frederick Muriuki
* gn3/computations/qtlreaper.py: handle exceptions Sometimes, the values being parsed are plain strings and cannot be cast to the float types. This commit handles that by casting only those values that can be cast to float, and returning the others as strings.
2021-09-06Find nearest markerMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Migrate the `web.webqtl.heatmap.Heatmap.getNearestMarker` function in GN1 to GN3.
2021-08-31Fix linting errors, minor bugs and reorganise codeMuriithi Frederick Muriuki
* Fix some linting errors and some minor bugs caught by the linter. Move the `random_string` function to separate module for use in multiple places in the code.
2021-08-31Update `heatmap_data` function: remove extraneous dataMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/heatmap.py: update function * gn3/db/traits.py: new function Remove extraneous data and arguments from the function. - Load the genotype file - Generate traits file - Provide both raw traits data, and exported traits data in return
2021-08-31Parse QTLReaper outputsMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/qtlreaper.py: pass output files * tests/unit/computations/data/qtlreaper/main_output_sample.txt: sample test data * tests/unit/computations/data/qtlreaper/permu_output_sample.txt: sample test data * tests/unit/computations/test_qtlreaper.py: add tests Add code to parse the QTLReaper output data files.
2021-08-31Fix bugs with `run_reaper` functionMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/qtlreaper.py: Fix some bugs * qtlfilesexport.py: Test out running rust-qtlreaper Test out the qtlreaper interface code and fix some bugs caught in the process.
2021-08-30Fix issues with traits file formatMuriithi Frederick Muriuki
* README.md: update header: Traits ==> Trait * gn3/computations/qtlreaper.py: update header: Traits ==> Trait * qtlfilesexport.py: Choose only BXD strains Rename the first column header from "Traits" to "Trait" to correspond with what `rust-qtlreaper` expects. Choose only the BXD strains for the proof-of-concept example - this helped bring out the fact that the traits file SHOULD NOT contain a strain column for a strain that does not exist in the genotype file in consideration. If the traits file has a strain column which does not exist in the genotype file, then `rust-qtlreaper` fails with a panic, since, from what I can tell, it tries to get a value from the genotype file for the non-existent strain, which results to a `None` type. Subsequent attempts at running an operation on the `None` type lead to the panic.
2021-08-30Remove empty lineMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Remove empty line at the end of the traits file
2021-08-30Fix some linting errors and minor bugs.Muriithi Frederick Muriuki
2021-08-30Implement module for interfacing with rust-qtlreaperMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/heatmap.py: move `generate_traits_file` function to new module * gn3/computations/qtlreaper.py: new module to interface with the `rust-qtlreaper` utility. * gn3/settings.py: Provide setting for the path to the `rust-qtlreaper` utility * qtlfilesexport.py: Move `random_string` function to new module. Update to use functions in new module. Provide a module with functions to be used to interface with `rust-qtlreaper`. This module essentially contains all the functions that are needed to build the files needed for, and to run the qtlreaper utility.
2021-08-27Provide intermediate data in final resultsMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Seeing as not every requirement/feature has been migrated over at this time, this commit just provides all the intermediate data representations in the final return of the function for later use down the line.
2021-08-27Export trait data to fileMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Provide a function to export the given strains and traits data into a traits file for use with `rust-qtlreaper`.
2021-08-27Rework strains and trait values retrievalMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Rework the strains and values retrieval function to more closely correspond to the working of the original code in GN1
2021-08-20Merge branch 'main' of github.com:genenetwork/genenetwork3 into ↵Muriithi Frederick Muriuki
heatmap_generation
2021-08-20Fix typing issue(s) caught by mypyMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/heatmap.py: Use `Sequence` type not `Iterator` type
2021-08-20Retrieve the strains with valid valuesMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/heatmap.py: add function to get strains with values * tests/unit/computations/test_heatmap.py: new tests Add function to get the strains whose values are not `None` from the `trait_data` object passed in. This migrates https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/Heatmap.py#L215-221 into a separate function that can handle that and be tested independently of any other code.
2021-08-20Add tests for ordering and implement functionMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/heatmap.py: implement new ordering function * tests/unit/computations/test_heatmap.py: add new tests Implement the ordering function to migrate the setup of the `neworder` variable from GN1 to GN3. This migration is incomplete, since there is dependence on the return from the `web.webqtl.heatmap.Heatmap.draw` function in form of the `d_1` variable in some of the paths. The thing is, this `d_1` variable, and the `xoffset` variable seem to be used for laying out things on the drawn heatmap, and might actually end up not being needed for the new system using plotly, which has other ways of laying out things on the drawing. For now though, this commit "shims" the presence of these values until when the use of these variables is confirmed as present or absent in the new GN3 system.
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.
2021-08-18Fix obvious linting errorsMuriithi Frederick Muriuki
* Fix linting errors that do not change the function of the code.
2021-08-18Make child sequence a listMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Since the `slink` function assigns values to the `listcopy` variable and its children, this commit ensures that the sequence is a list to allow for the assignment. If the child-sequence is a tuple, that would lead to an exception.
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
2021-08-17Test 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.
2021-08-17Fix obvious linting errorsMuriithi Frederick Muriuki
* Fix linting errors that do not change the function of the code.
2021-08-17Make child sequence a listMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Since the `slink` function assigns values to the `listcopy` variable and its children, this commit ensures that the sequence is a list to allow for the assignment. If the child-sequence is a tuple, that would lead to an exception.
2021-08-17Add 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
2021-08-16Merge pull request #32 from genenetwork/heatmap_decompose_db_retrievalBonfaceKilz
Heatmap decompose db retrieval
2021-08-12Fix linting errorsMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Fix some errors caught by the linter.
2021-08-12Import missing definitionsMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Import some missing definitions.
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
2021-08-09Build up the heatmap dataMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Add code to compute and organise the data that will be used to draw the final heatmap. This varies significantly in how it works from the original, but it still tries to retain the general flow of data.
2021-08-04Fix issues caught by pylintMuriithi Frederick Muriuki
* gn3/computations/slink.py: remove unused imports * gn3/db/traits.py: remove unnecessary `else` clauses * tests/unit/db/test_traits.py: add docstrings for functions
2021-07-29Add partial type annotations for slink moduleMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Add some type annotations for the `nearest` function. * Leave some comments regarding the issues experienced when trying to add some typing annotations to the function to help with future endeavours of the same.
2021-07-29Add partial type annotations for slink moduleMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Add some type annotations for the `nearest` function. * Leave some comments regarding the issues experienced when trying to add some typing annotations to the function to help with future endeavours of the same.
2021-07-26Merge branch 'main' of github.com:genenetwork/genenetwork3Muriithi Frederick Muriuki
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.
2021-07-26Check if corr_coefficient is NaN, since apparently it's stored as NaN ↵zsloan
instead of None when it can't be calculcated (which was messing up sorting); it may also be okay to remove the None check, but leaving it for now (#28)
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
2021-07-23Iterate through all valid pairsMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/slink.py: Fix the iteration construct. Given two lists of member coordinates, such as [0, 1] and [3, 5], the initial code would iterate over the pairs [0, 3] and [1, 5]. This commit fixes the iteration constructs such that the new code iterates over the pairs [0, 3], [0, 5], [1, 3] and [1, 5].
2021-07-23Extract function to flatten list of listsMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/slink.py: Extract the `__flatten_list_of_lists` function since it is used in more than one place.
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.
2021-07-23Add dummy module documentationMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/slink.py: Add initial dummy module documentation in form of a python docstring Update the names of what would be private methods/function to start with a double-underscore (__) so that they do not show up in the default python documentation.
2021-07-23Add docstring for `nearest' functionMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/slink.py: add documentation for the `nearest` function in the `gn3.computations.slink` module in the form of a (hopefully correct) python docstring.
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