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2024-11-11Refactor: refactor checks for working directory, input and output file.Alexander_Kabui
2024-11-11refactor: remove stringr as a script dependency:Alexander_Kabui
refactor: refactor use of str_glue to cat.
2024-11-11refactor: refactor for using cat and new line.Alexander_Kabui
2024-11-11refactor: use NO_OF_CORES as default and pass control file to arguments.Alexander_Kabui
2024-11-11refactor: adding pseudomarkers o genetic probabilites map.Alexander_Kabui
2024-11-11refactor: refactor printing out lod thresholds.Alexander_Kabui
2024-11-11export qtl effect plots for multi parent populations.Alexander_Kabui
2024-11-11feat: add plots for qtl effect multi parent population.Alexander_Kabui
2024-11-11feat: implementation for getting meffects for multiparent population.Alexander_Kabui
2024-11-11feat: implementation for multiparent genome scan.Alexander_Kabui
2024-11-11feat: export chromosome names and qtl effects.Alexander_Kabui
2024-11-08feat: init add functionality to estimate qtl effect.Alexander_Kabui
2024-10-30feat: add option for using pstrata for permutation.Alexander_Kabui
2024-10-30Refactor: Remove reduntant code.Alexander_Kabui
Fix issue when computing the kinship
2024-10-29Refactor: pre compute kinship for both permutation and genome scan.Alexander_Kabui
2024-10-29Refactor: remove hardcoded dir_path for control files.Alexander_Kabui
2024-10-29Refactor: make plot in the temp directory passed in the script arguments.Alexander_Kabui
2024-10-29feat: add output_file as a command line argument.Alexander_Kabui
2024-10-29Refactor: ensure the temp directory is not null.Alexander_Kabui
ensure the input_file exists in the working directory.
2024-10-29feat: add optparse for the arguments.Alexander_Kabui
2024-10-29feat: write output results as json.Alexander_Kabui
2024-10-29Refactor: refactor code to find lod peaks.Alexander_Kabui
2024-10-29Refactor: refactoring for code to perform permutation tests.Alexander_Kabui
2024-10-29Refactor: refactor function to generate plots from scan1 function.Alexander_Kabui
2024-10-29Refactor: refactor method to compute scan 1.Alexander_Kabui
2024-10-29Refactor: refactor function to calculate error LOD scores.Alexander_Kabui
2024-10-29Refactor: refactor functions to compute genetic probabilities:Alexander_Kabui
2024-10-29Refactor: cleanup comments.Alexander_Kabui
2024-10-29Refactor: use FALSE for better defaults.Alexander_Kabui
2024-10-29feat: add defaults for creating cross objects.Alexander_Kabui
2024-10-28refactor: Minor fixes for file, remove commentsAlexander_Kabui
2024-10-25feat: add function to fetch load peaks for 1 QTL.Alexander_Kabui
2024-10-25Minor fix.Alexander_Kabui
2024-10-25Refactor: apply code formatting.Alexander_Kabui
2024-10-25feat: add code to perform permutation for single Qtl.Alexander_Kabui
2024-10-25feat: add method to generate LOD curves for the genome scan.Alexander_Kabui
2024-10-25feat: Add method to perform 1 pair scan.Alexander_Kabui
2024-10-25feat: add code to perform genetic probabilities.Alexander_Kabui
2024-10-24feat: create implementation for creating cross object using r-qtl2.Alexander_Kabui
2024-10-18refactor: replace gn3.auth.db with gn3.sqlite_db_utils and drop all refs to ↵John Nduli
gn3.auth
2024-10-18refactor: move definition of auth errs and remove auth cli utilsJohn Nduli
2024-10-18refactor: remove unused gn3.auth modulesJohn Nduli
2024-10-15Lint: Fix linting errors.Frederick Muriuki Muriithi
2024-10-15Pass in correct file path.Frederick Muriuki Muriithi
2024-10-15fix: use require_token to validate gn3 apisJohn Nduli
2024-10-14Run python black against file.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-10-14Replace CONSTRUCT with SELECT for fetching RIF NCBI entries.Munyoki Kilyungi
* gn3/db/rdf/wiki.py: Delete datetime import. Import sparql_query. [RIF_CONTEXT]: Delete. (get_rif_entries_by_symbol): Replace CONSTRUCT with SELECT. * tests/unit/db/rdf/test_wiki.py (test_get_rif_entries_by_symbol): Update tests. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-10-14Replace species' shortName with it's full name in NCBI test data.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-10-14Remove "@id" from NCBI test data.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-10-14Update the NCBI expected test data context.Munyoki Kilyungi
* tests/unit/db/rdf/data.py: [LPL_RIF_ENTRIES]: Update "@context". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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