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path: root/gn3/db/genotypes.py
AgeCommit message (Expand)Author
2023-10-06Make argument mandatory...Make the `base_dir` argument mandatory to force it to be passed in from the point the function is called. Frederick Muriuki Muriithi
2022-03-11Fix typing errorsFrederick Muriuki Muriithi
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
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
2021-09-22Fix more pylint errorsFrederick Muriuki Muriithi
2021-09-22Fix typing issues...* Ignore some errors * Update typing definitions for some portions of code * Add missing imports Frederick Muriuki Muriithi
2021-09-22Fix pylint errors...* Add missing function and module docstrings * Remove unused imports * Fix import order * Rework some code sections to fix issues * Disable some pylint errors. Frederick Muriuki Muriithi
2021-09-17Fix a number of linting issues...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi Frederick Muriuki Muriithi
2021-09-01Fix linting and typing issues...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi Muriithi Frederick Muriuki
2021-09-01Built top-level genotype file parsing function...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/db/genotypes.py: parse genotype files * tests/unit/db/test_genotypes.py: test parsing is correct Add the overall genotype files parsing function and tests to check that the parsing works as expected. Muriithi Frederick Muriuki
2021-09-01Parse data lines into markers...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/db/genotypes.py: parse data lines in file to genetic markers. * tests/unit/db/test_genotypes.py: test that parsing works. Add some tests to check that the parsing of the markers works as expected, and add the code to actually parse the markers. Muriithi Frederick Muriuki
2021-09-01Parse the genotype file's data header...* gn3/db/genotypes.py: parse data header * tests/unit/db/test_genotypes.py: check that header's parse works correctly. Add tests to check that the parser works as expected. Add code to implement the parsing and pass the tests. Muriithi Frederick Muriuki
2021-09-01Implement parsing of genotype labels...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/db/genotypes.py: parse genotype labels * tests/unit/db/test_genotypes.py: test that genotype labels are parsed correctly As part of parsing the genotype files into usable python data structures, this commit adds a function to parse the label lines (beginning with "@") into the appropriate values. Muriithi Frederick Muriuki
2021-08-31Provide utilities for genotype files...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/db/genotypes.py: New module * gn3/settings.py: Add new configuration variable * qtlfilesexport.py: Test out new code Add a module containing functions dealing with the genotype files. Add a configuration variable to point to the location of the genotype files. Muriithi Frederick Muriuki