genenetwork3/scripts, branch technical-specificationGeneNetwork3 REST API for data science and machine learning
http://git.genenetwork.org/genenetwork3/atom?h=technical-specification2022-03-22T20:39:22+00:00Merge 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:a75634cc5637168165e601f09dc9ad820e6e443fChange order of if statements for running genoprob command2022-03-22T20:28:58+00:00zsloan2022-03-22T20:28:58+00:00urn:sha1:0e6990940e22eb0431d6a27e45d29bc04d8ad582
Now it checks for pairscan first, just in case interval ends up being
passed (which is an irrelevant parameter for pairscan)
Also added a couple more verbose prints
Updated rqtl_wrapper to also return a map file when doing a pair-scan (since we need the list of markers/pseudomarkers and their positions)2022-03-22T19:08:01+00:00zsloan2021-08-02T21:07:52+00:00urn:sha1:4c3359082fbb1eef93a9e54c633f938606cba5f6Added line priting pair-scan results to CSV and changed the default step-size to 10cM for pair-scan2022-03-22T19:07:00+00:00zsloan2021-07-23T20:08:36+00:00urn:sha1:acfea0fc8793372723be0e64316002ed9bc2403b- Added scan_func function that determines whether scanone or scantwo2022-03-22T19:05:37+00:00zsloan2021-07-23T19:40:04+00:00urn:sha1:2849792ddc2e76750421c75d926d5a7f18c57e97
(pairscan) is used
- For pairscan default to using step 20 (subject to change, but some
step is required during calc.genoprob to make it run fast enough)
- Added some new verbose prints
Added option for running pairscan to rqtl_wrapper.R2022-03-22T19:03:23+00:00zsloan2021-07-22T23:47:58+00:00urn:sha1:e13e10d0f0dc96518e1d5efa9865ac2821b1c3f9Create database connections within context managers2022-03-08T05:00:16+00:00Frederick Muriuki Muriithi2022-03-08T05:00:16+00:00urn:sha1:eae345ed252c01e541d64c7e5b60b488d84268c6
Use the `with` context manager to open database connections, so as to ensure
that those connections are closed once the call is completed. This hopefully
avoids the 'too many connections' error
Run partial correlations in an external process2022-03-03T07:20:04+00:00Frederick Muriuki Muriithi2022-02-23T11:51:47+00:00urn:sha1:6d39c92fbc9a7b82cd8eef60c62cd5d83acb49a1
Run the partial correlations code in an external python process decoupling it
from the server and making it asynchronous.
Summary of changes:
* gn3/api/correlation.py:
- Remove response processing code
- Queue partial corrs processing
- Create new endpoint to get results
* gn3/commands.py
- Compose the pcorrs command to be run in an external process
- Enable running of subprocess commands with list args
* gn3/responses/__init__.py: new module indicator file
* gn3/responses/pcorrs_responses.py: Hold response processing code extracted
from ~gn3.api.correlations.py~ file
* scripts/partial_correlations.py: CLI script to process the pcorrs
* sheepdog/worker.py:
- Add the *genenetwork3* path at the beginning of the ~sys.path~ list to
override any GN3 in the site-packages
- Add any environment variables to be set for the command to be run
Quote shell variables to prevent globbing2022-02-11T02:52:36+00:00Frederick Muriuki Muriithi2022-02-11T02:45:24+00:00urn:sha1:651c8ad9ae20ab52e7ab694c0caa9d92774b49b5
Quote the shell variables to prevent globbing and word splitting.
Deactivate this check for the specific lines that require intentional word
splitting
Fix R/qtl covar bug2022-02-02T20:15:25+00:00zsloan2022-02-02T20:10:00+00:00urn:sha1:750bc975650d27e67d1d0b3f6ecaab6582304b44
The rqtl_wrapper script was throwing an error when only a single
categorical covariate was used. This is apparently because "covars[,name]"
throws an error in such a situation. Using just "covars" in such a
situation prevents the error. So I just added an if statement checking
the number of covariates. There might be some better way to deal with
this in R, but this is the best I could come up with.