genenetwork3/scripts, branch data-access-levels-endpointGeneNetwork3 REST API for data science and machine learning
http://git.genenetwork.org/genenetwork3/atom?h=data-access-levels-endpoint2023-02-13T17:36:09+00:00scripts: Fallback to 1 worker when indexing.2023-02-13T17:36:09+00:00Arun Isaac2023-02-13T17:35:13+00:00urn:sha1:283e7f08701ed80cdfeb8773df38c0c30227a10c
* scripts/index-genenetwork (worker_queue): Set default number of workers to 1
if the number of CPUs cannot be determined.
scripts: Type hint xapian indexing script.2023-02-13T17:36:09+00:00Arun Isaac2023-02-13T17:33:27+00:00urn:sha1:152d0fb36b76b7c68d8202ba3665617bad3e684b
* scripts/index-genenetwork: Import Callable, Generator, Iterable and List
from typing. Type hint all functions.
Add xapian indexing script.2022-10-18T12:15:33+00:00Arun Isaac2022-10-18T09:10:47+00:00urn:sha1:06da0390a1de5d0aa8eb6d7a0ed3120e350f8a0b
* scripts/index-genenetwork: New file.
* setup.py (install_requires): Add click, pymonad and xapian-bindings.
(scripts): Add scripts/index-genenetwork.
New script to run sample correlations2022-07-29T01:00:41+00:00Frederick Muriuki Muriithi2022-07-29T01:00:41+00:00urn:sha1:6b11a267084c131ac7e1be76c4eb602996fd829e
* README.md: update mypy's invocation
* scripts/argparse_actions.py: new file - implement custom FileCheck action
for argparse
* scripts/sample_correlations.py: new file - implement new script to run
sample correlations in an external process
Parse the method from UI before passing it to external process2022-06-28T06:32:14+00:00Frederick Muriuki Muriithi2022-06-28T06:32:14+00:00urn:sha1:d8d590cbc0a427c2f508c66bc91cd8af97aba606
To reduce the chances of the system failing due to the external process being
launched with the wrong parameters, add a parsing stage that converts the
method from the UI into a form acceptable by the CLI script.
* gn3/commands.py: parse the method from UI
* scripts/partial_correlations.py: simplify the acceptable methods
Restrict partial correlation method choices2022-06-20T08:17:11+00:00Frederick Muriuki Muriithi2022-06-20T08:17:11+00:00urn:sha1:7f66bb029322a06b52359abf8836e158afaa6755
- Have "Pearson's r" and "Spearman's rho" as the only valid choices for the
partial correlations
Run partial correlations with external script2022-05-24T11:19:57+00:00Frederick Muriuki Muriithi2022-05-24T11:19:57+00:00urn:sha1:fdf9061981ce5d341d178951adeb19dd0376ee66
Use new external script to run the partial correlations for both cases,
i.e.
- against an entire dataset, or
- against selected traits
New script to compute partial correlations2022-05-24T02:16:55+00:00Frederick Muriuki Muriithi2022-05-24T01:46:57+00:00urn:sha1:36f8421a8fe223189ab88ee1df3923719ffa4fc0
* Add a new script to compute the partial correlations against:
- a select list of traits, or
- an entire dataset
depending on the specified subcommand. This new script is meant to supercede
the `scripts/partial_correlations.py` script.
* Fix the check for errors
* Reorganise the order of arguments for the
`partial_correlations_with_target_traits` function: move the `method`
argument before the `target_trait_names` argument so that the common
arguments in the partial correlation computation functions share the same
order.
Extract common error checking. Rename function.2022-05-05T12:19:08+00:00Frederick Muriuki Muriithi2022-05-05T12:19:08+00:00urn:sha1:be9d1d4aad720274f6d75345123fae8d6a96bc12
* Extract the common error checking code into a separate function
* Rename the function to make its use clearer
Merge branch 'feature/add_rqtl_pairscan' of https://github.com/zsloan/genenetwork3 into feature/add_rqtl_pairscan2022-03-22T20:39:22+00:00zsloan2022-03-22T20:39:22+00:00urn:sha1:a75634cc5637168165e601f09dc9ad820e6e443f