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2021-06-18db: phenotypes: Rename phenotype_column_mappingBonfaceKilz
2021-06-18db: phenotypes: Add Publication dataclass and mappingBonfaceKilz
2021-06-18db: phenotypes: Generalise the update functionBonfaceKilz
* gn3/db/phenotypes.py (update_phenotype): Delete it. (update): New, more general function.
2021-06-18db: phenotypes: Map a table to it's relevant dict mappingBonfaceKilz
2021-06-18db: phenotypes: Add type for DataclassBonfaceKilz
See: https://www.py4u.net/discuss/188952
2021-06-18db: phenotypes: Put mapping def after dataclassBonfaceKilz
2021-06-18db: phenotypes: Add phenotype table mappingBonfaceKilz
2021-06-18db: phenotypes: Add dataclass to represent PublishXRefBonfaceKilz
2021-06-18db: phenotype: Make "pylint: disable=[R0902]" global for fileBonfaceKilz
2021-06-18db: phenotypes: Add a way of updating the Phenotype tableBonfaceKilz
* gn3/db/phenotypes.py (Phenotype): New dataclass. (update_phenotype): New function. [phenotype_column_mapping]: New variable.
2021-06-18Fixed issue where all bool kwargs were always being passed to ↵zsloan
generate_rqtl_cmd and also made code check if output file already exists (so caching works)
2021-06-18Fix R/qtl command and the way keyword arguments are passedzsloan
2021-05-25Include code that processes rqtl output files and returns actual results ↵zsloan
instead of just the output filename
2021-05-19Temporarily replace forward-slashes with underscores, since they can be ↵zsloan
included in the hashes used for filenames
2021-05-18Removed len from this if statement, since an empty list evaluates to False ↵zsloan
by itself
2021-05-18Account for boolean kwargs in compute() by storing them in a list, since ↵zsloan
they don't have corresponding values
2021-05-18Account for boolean kwargs in compose_rqtl_cmdzsloan
2021-05-18Fixed generate_rqtl_cmd to make the kwarg hash from a combination of ↵zsloan
keywords and arguments + account for boolean kwargs without values (like --interval or --covar)
2021-05-18Fixed variety of issues detected by pylintzsloan
2021-05-17Created compose_rqtl_command and generate_rqtl_command to create the actual ↵zsloan
command to be run from the command line; used the same pattern as for GEMMA for consistency
2021-05-17Read in kwargs fromrequest and pass the command, tmpdir, and kwargs to ↵zsloan
generate_rqtl_cmd which returns the actual command and output path
2021-05-17Added RQTL_WRAPPER_CMD (which is fetched from environment) in settings.pyzsloan
2021-05-17Add rqtl.py for rqtl endpointszsloan
2021-05-17Register rqtl blueprintzsloan
2021-05-15resolve merge conflictAlexander Kabui
2021-05-15Merge branch 'main' into feature/minor-fixesAlexander Kabui
2021-05-15index lit tuple resultAlexander Kabui
2021-05-13Add end-point for running an rQTL programBonfaceKilz
* gn3/api/general.py (run_r_qtl): New function. * gn3/settings.py: New variable.
2021-05-13Rename file_utils to fs_helpersBonfaceKilz
Generally avoid naming things with a "utils" prefix/ suffix since it encourages contributors to dump any new functions there; and over time, as the code grows, things get messy...
2021-05-13computations: correlations: Apply pep-8BonfaceKilz
2021-05-12delete unused functionsAlexander Kabui
2021-05-12rename lit_correlation_for_trait_list to lit_correlation_for_traitAlexander Kabui
2021-05-12rename tissue_correlation_for_trait_list with tissue_correlation_for_traitAlexander Kabui
2021-05-12rename p_val ro tissue_p_value for tissue_resultsAlexander Kabui
2021-05-10db: species: Add method for fetching all speciesBonfaceKilz
2021-05-08db: species: Fetch chromosomes using a group or species nameBonfaceKilz
* gn3/db/species.py (get_chromosome): New function.
2021-05-08gn3: db_utils: Remove mypy ignore stubBonfaceKilz
MySQLdb is already ignored in ".mypy.ini", added in 88c33df.
2021-05-08Fix pep-8 errorsBonfaceKilz
2021-05-08db: traits: Add extra method for looking up webqtl datasetsBonfaceKilz
2021-05-08db: traits: Update method for inserting publication methodBonfaceKilz
2021-05-08Add method for inserting publication_dataBonfaceKilz
2021-05-08Add webqtlCaseData DS to keep track of case data in one traitBonfaceKilz
2021-05-08Replace namedtuple with a dataclassBonfaceKilz
2021-05-08Add method for inserting phenotypesBonfaceKilz
2021-05-08Add method for inserting publicationsBonfaceKilz
2021-05-08Add method to fetch riset name and idBonfaceKilz
2021-05-08Add endpoints for (batch) entering phenotypes and genotypesBonfaceKilz
2021-05-08Add extra procedure for parsing a genotype fileBonfaceKilz
* gn3/computations/parsers.py (parse_genofile): New procedure. * tests/unit/computations/test_parsers.py: New test files for above.
2021-05-03add default no of coresAlexander Kabui
2021-05-03modify default SQL_URIAlexander Kabui
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