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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
2021-09-23Fix issue that causes R/qtl to always run pair-scan even if pair-scan isn't ↵zsloan
selected
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
2021-09-23Fix imports to import both process_rqtl_mapping and process_rqtl_pairscan in ↵zsloan
api/rqtl.py
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
2021-08-20Minor 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.
2021-08-18Provide top-level `riset` key-value pairMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Provide the expected, top-level `riset` key-value pair and eliminate the redundant key-value pair.
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
2021-08-18Fix errors: add in missing parenthesisMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Call the `cursor.fetchone()` function to get results. Without the parenthesis, the code was trying to use the function itself as the results, which was a bug, and would lead to failure.
2021-08-18Initialise heatmap generation moduleMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/heatmaps/heatmaps.py: Initialise the module with some code to be used to test out plotly features on the command-line. * guix.scm: Add `python-plotly` and `python-pandas` as dependencies.
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.
2021-08-09Set up the trait dataset type correctlyMuriithi Frederick Muriuki
* gn3/db/traits.py: setup `trait_dataset_type` * tests/unit/db/test_traits.py: fix tests The type ('Temp', 'Geno', 'Publish', and 'ProbeSet') relate to a trait's dataset, and not the trait itself. This commit updates the code to take this into consideration. The dataset type is also set up from a trait's full name, therefore this commit removes the `trait_type` argument from the `retrieve_trait_info` function.
2021-08-09Retrieve the trait dataMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Add functions to retrieve the `value`, `variance`, and `ndata` values for any given trait.
2021-08-09Add missing arguments. Fix typo.Muriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Fix minor bugs in the code.
2021-08-09Fix linting errorsMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Add module, class and function docstrings * Deactivate some irrelevant pylint errors * Fix indentations and line-lengths
2021-08-08Only load extra data if the traits have basic infoMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Only load the extra trait data if the basic trait information is found.
2021-08-08Merge branch 'main' of github.com:genenetwork/genenetwork3 into ↵Muriithi Frederick Muriuki
heatmap_decompose_db_retrieval
2021-08-07Add gunicorn support for productionPjotr Prins
2021-08-05db: traits: Return unique values when fetching sample dataBonfaceKilz
2021-08-05Reorganise the database codeMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Reorganise the code to separate the datasets from the traits, and to more closely conform to the same flow as that in GN1
2021-08-05Build up trait_name items from full nameMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * The full name of the traits from search contains multiple parts to it, and as such, we use it to retrieve the appropriate data and set it up in the final trait_info dictionary that is produced.
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
2021-08-04Retrieve the RISet and RISet ID valuesMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Retrieve the RISet and RISet ID values from the database.
2021-08-04Add tests for post-processing functionsMuriithi Frederick Muriuki
Issues: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Add missing tests for some post-processing functions
2021-08-04Avoid string interpolation: use prepared statementMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Following Arun's comment at https://github.com/genenetwork/genenetwork3/pull/31#issuecomment-890915813 this commit eliminates string interpolation, and adds a map of tables for the various types of traits dataset names
2021-08-03Create 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
2021-07-30Rework db functions to enable postprocessingMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Rework the database functions to return a dict of key-value pairs, which eases the postprocessing of the trait information. The postprocessing is mainly to try an maintain data compatibility with the code that is at the following locations: https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlDataset.py https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/Heatmap.py This was mainly a proof-of-concept, and the functions do not have testing added for them: there is therefore need to add testing for the new functions, and probably even rework them if they are found to be complicated.
2021-07-30Add module for common utilitiesMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/function_helpers.py: new file Provides a new module to hold common programming utilities that are generic enough that they will find use across the entire application. The first utility function provided in this commit is the `compose` function, whose purpose, as indicated by its name, is to take a number of functions and compose them into a single function, which when called, will return the same result that would have been got had the user called the functions in a chain from right to left.
2021-07-30Return dict from query functionsMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/db/traits.py: return dicts rather than tuples/list * tests/unit/db/test_traits.py: Update tests Return dicts with the key-value pairs set up so as to ease with the data manipulation down the pipeline. This is also useful to help with the retrieval of all other extra information that was left out in the first iteration. This commit also updates the tests by ensuring they expect dicts rather than tuples.
2021-07-29Fix imports to import both process_rqtl_mapping and process_rqtl_pairscan in ↵zsloan
api/rqtl.py
2021-07-29Merge branch 'main' into Feature/Update-db-from-csv-dataBonfaceKilz
2021-07-29Delete "update_raw" and it's test-casesBonfaceKilz
2021-07-29Add method for updating values from a sample datasetBonfaceKilz
* gn3/db/traits.py (update_sample_data): New function. * tests/unit/db/test_traits.py: New test cases for ^^.
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 type annotations to the functionMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Add some type annotations to the functions to reduce the chances of bugs creeping into the code.
2021-07-29Retrieve trait informationMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/db/traits.py: add functions to retrieve traits information * tests/unit/db/test_traits.py: add tests for new function Add functions to retrieve traits information as is done in genenetwork1 https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L397-L456 At this point, the data retrieval functions are probably incomplete, as there is more of the `retrieveInfo` function in GN1 that has not been considered as of this commit.
2021-07-29Make name retrieval more generalMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/db/traits.py: make function more general * tests/unit/db/test_traits.py: parametrize the tests Make the name retrieval more general for the different types of traits by changing the column specification and table as appropriate.
2021-07-29Retrieve 'ProbeSet' trait nameMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/db/traits.py: new function (retrieve_probeset_trait_name) * tests/unit/db/test_traits.py: test(s) for new function Add a function to retrieve the name of a 'ProbeSet' trait in a manner similar to genenetwork1's retrieval of the same, as implemented here https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlDataset.py#L140-154 Unlike in genenetwork1, we do not mutate an object, instead, we return the values as retrieved from the database, and the caller will deal with the returned values as appropriate.
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