| Age | Commit message (Collapse) | Author |
|---|
|
* scripts/index-genenetwork: Import Callable, Generator, Iterable and List
from typing. Type hint all functions.
|
|
* scripts/index-genenetwork: New file.
* setup.py (install_requires): Add click, pymonad and xapian-bindings.
(scripts): Add scripts/index-genenetwork.
|
|
* 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
|
|
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
|
|
- Have "Pearson's r" and "Spearman's rho" as the only valid choices for the
partial correlations
|
|
Use new external script to run the partial correlations for both cases,
i.e.
- against an entire dataset, or
- against selected traits
|
|
* 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 the common error checking code into a separate function
* Rename the function to make its use clearer
|
|
https://github.com/zsloan/genenetwork3 into feature/add_rqtl_pairscan
|
|
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
|
|
we need the list of markers/pseudomarkers and their positions)
|
|
step-size to 10cM for pair-scan
|
|
(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
|
|
|
|
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 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 the shell variables to prevent globbing and word splitting.
Deactivate this check for the specific lines that require intentional word
splitting
|
|
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.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
* add r as a gn3 input
* calculate powers from user input
* fix merge conflict
|
|
|
|
* add biweight reimplementation with pingouin
* delete biweight scripts and tests
* add python-pingouin to guix file
* delete biweight paths
* mypy fix:pingouin mising imports
* pep8 formatting && pylint fixes
|
|
|
|
|
|
|
|
|
|
bug/fix_rqtl_covariates
|
|
feature/add_rqtl_pairscan
|
|
|
|
we need the list of markers/pseudomarkers and their positions)
|
|
step-size to 10cM for pair-scan
|
|
(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
|
