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2024-09-12Fix failing tests after merging in Pjotr's pull request.Frederick Muriuki Muriithi
2024-09-12From gn3 only use TMPDIR/gn3 pathsPjotr Prins
2024-09-12Replace TMPDIR/output with TMPDIR/gn3 so it is clear where it comes fromPjotr Prins
2024-09-12Modify script paths so they can be edited in GuixPjotr Prins
2024-09-12Make sure TMPDIR directories exist!Pjotr Prins
2024-09-12Move assert_paths_exist into fs_helpersPjotr Prins
2024-09-12Change behavior of do_paths_exist to actually throw useful errorPjotr Prins
2024-09-12Getting Rqtl to run on fallbackPjotr Prins
2024-09-12Move assert_paths_exist into fs_helpersPjotr Prins
2024-09-12Change behavior of do_paths_exist to actually throw useful errorPjotr Prins
2024-02-25Disable too-many-arguments for "run_reaper".Munyoki Kilyungi
* gn3/computations/qtlreaper.py: Disable "too-many-arguments" pylint check. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-02-19Pass qtlreaper command path as argument to run_reaperzsloan
Originally the system would get the path from the environment
2023-10-27Remove reimport "Optional".Munyoki Kilyungi
* gn3/computations/gemma.py: Delete reimport "Qptional". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Make implicit optional type hints PEP 484 compliant.Munyoki Kilyungi
Ran the command: pipx run no_implicit_optional ./ in the root directory.
2023-10-26Fix errors caught by mypy.Frederick Muriuki Muriithi
2023-10-06pylint: fix variable name.Frederick Muriuki Muriithi
2023-10-06Get `CORRELATION_COMMAND` from current_app not `gn3.settings`Frederick Muriuki Muriithi
The default settings in `gn3.settings` are meant to be overridden thus the code should not be importing the setting from there, rather, the code should get its configurations settings from `flask.current_app.config`.
2023-09-05Fix C3001: Lambda expression assigned to a variableMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-01-25Some commentsPjotr Prins
2022-12-21gn3: (gn3.random -> gn3.chancy): Rename module to avoid conflicts.Frederick Muriuki Muriithi
Rename the `gn3.random` module to gn3.chancy to avoid conflicts with Python's `random` module. * gn3/random.py -> gn3/chancy.py: rename module * gn3/commands.py: update import * gn3/computations/partial_correlations.py: update import * gn3/computations/qtlreaper.py: update import * gn3/computations/rust_correlation.py: update import * gn3/db/correlations.py: update import * gn3/db/traits.py: update import * gn3/heatmaps.py: update import * tests/integration/conftest.py: update import
2022-12-06mypy and pylint fixesAlexander_Kabui
2022-12-02correlations: return `None` rather than zero for missing lit corrsFrederick Muriuki Muriithi
* gn3/computations/correlations.py: Return `None` for missing literature correlations rather than zero. Update the sorting key to avoid issues with comparing floats to NoneType objects
2022-11-29remove trailing whitespaceAlexanderKabui
2022-11-29remove unused function parameterAlexanderKabui
2022-11-08Fix issue where only primary samples were used when all samples arezsloan
selected This is because base_samples was set to all_samples_ordered, which only includes primary samples + parents/f1s. Setting this to an empty list fixed the issue and caused it to use all samples again.
2022-10-22fix issue;parsing sample data (#102)Alexander Kabui
2022-10-06DEBUG: Collect more info for debuggingFrederick Muriuki Muriithi
2022-10-06DEBUG: Collect more information on possible failure.Frederick Muriuki Muriithi
2022-10-03Bug: Do not process data for output too earlyFrederick Muriuki Muriithi
* gn3/computations/rust_correlation.py: (parse_tissue_corr_data): The function was parsing data from a file, and then converting the parsed values into a comma-separated string for output, despite the fact that the data parsed is not output in this specific function. This is a really bad idea, and leads to errors showing up down the line, far removed from the cause.
2022-09-30Add escape char to avoid error notice.Frederick Muriuki Muriithi
2022-09-29Use the built-in csv module for file outputFrederick Muriuki Muriithi
Use the built-in csv module for file output in order to avoid subtle errors in the formats.
2022-08-25revert for commit 6db3b2af8fc09999996d3acc09890a06f179c669;BugAlexander_Kabui
2022-08-12Add mandatory/expected fields to parsed data.Frederick Muriuki Muriithi
2022-08-10Fix returned value for 'parse_correlation_output'Frederick Muriuki Muriithi
* Always return dict * Fix internal '__parse_line__' to always have a valid return
2022-08-10code refactoringFrederick Muriuki Muriithi
2022-08-10remove unnecessary parsing of floatsAlexander_Kabui
2022-08-10code refactoringFrederick Muriuki Muriithi
2022-08-10remove unnecessary parsing of floatsAlexander_Kabui
2022-08-10enhancements for rust tissueFrederick Muriuki Muriithi
2022-08-10pylint fixesAlexander_Kabui
2022-08-10code refactoringAlexander_Kabui
2022-08-10remove unnessary codeAlexander_Kabui
2022-08-10remove unnecessary parsing of floatsAlexander_Kabui
2022-08-10merge for resultsAlexander_Kabui
2022-08-10enhancements for rust tissueAlexander_Kabui
2022-08-03Refactor: Remove unnecessary whitespace and nameFrederick Muriuki Muriithi
2022-08-03Refactor: Remove unnecessary iterations and nameFrederick Muriuki Muriithi
* remove extra iteration that is unnecessary * remove unnecessary variables
2022-07-29Fix failing testsFrederick Muriuki Muriithi
* gn3/computations/correlations.py: rename function * mypy.ini: deactivate mypy error about missing imports * tests/integration/test_correlation.py: mock correct function * tests/unit/computations/test_correlation.py: test correct function
2022-07-28Update sample correlations code to use multiprocessingFrederick Muriuki Muriithi
* To help speed up the processing of the correlations, convert the `compute_all_sample_correlation` function to use the multiprocessing module.
2022-07-22mypy fixesAlexander_Kabui
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