| Age | Commit message (Expand) | Author |
|---|
| 2022-10-18 | Add xapian indexing script....* scripts/index-genenetwork: New file.
* setup.py (install_requires): Add click, pymonad and xapian-bindings.
(scripts): Add scripts/index-genenetwork.
| Arun Isaac |
| 2022-07-29 | New script to run sample correlations...* 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
| Frederick Muriuki Muriithi |
| 2022-06-28 | Parse the method from UI before passing it to 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
| Frederick Muriuki Muriithi |
| 2022-06-20 | Restrict partial correlation method choices...- Have "Pearson's r" and "Spearman's rho" as the only valid choices for the
partial correlations
| Frederick Muriuki Muriithi |
| 2022-05-24 | Run partial correlations with external script...Use new external script to run the partial correlations for both cases,
i.e.
- against an entire dataset, or
- against selected traits
| Frederick Muriuki Muriithi |
| 2022-05-24 | New script to compute partial correlations...* 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.
| Frederick Muriuki Muriithi |
| 2022-05-05 | Extract common error checking. Rename function....* Extract the common error checking code into a separate function
* Rename the function to make its use clearer
| Frederick Muriuki Muriithi |
| 2022-03-22 | Merge branch 'feature/add_rqtl_pairscan' of https://github.com/zsloan/genenet... | zsloan |
| 2022-03-22 | Change order of if statements for running genoprob command...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
| zsloan |
| 2022-03-22 | Updated rqtl_wrapper to also return a map file when doing a pair-scan (since ... | zsloan |
| 2022-03-22 | Added line priting pair-scan results to CSV and changed the default step-size... | zsloan |
| 2022-03-22 | - Added scan_func function that determines whether scanone or scantwo...(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
| zsloan |
| 2022-03-22 | Added option for running pairscan to rqtl_wrapper.R | zsloan |
| 2022-03-08 | Create database connections within context managers...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
| Frederick Muriuki Muriithi |
| 2022-03-03 | Run partial correlations in an external process...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
| Frederick Muriuki Muriithi |
| 2022-02-11 | Quote shell variables to prevent globbing...Quote the shell variables to prevent globbing and word splitting.
Deactivate this check for the specific lines that require intentional word
splitting
| Frederick Muriuki Muriithi |
| 2022-02-02 | Fix R/qtl covar bug...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.
| zsloan |
| 2022-02-02 | remove comments | Alexander Kabui |
| 2022-02-02 | match case string input to boolean | Alexander Kabui |
| 2022-02-02 | fix for parametric input | Alexander Kabui |
| 2022-02-02 | use user input significance | Alexander Kabui |
| 2022-02-02 | new line fix | Alexander Kabui |
| 2022-02-02 | add new json output | Alexander Kabui |
| 2022-01-22 | minor refactoring | Alexander Kabui |
| 2022-01-22 | function override:fix target specific output file for network | Alexander Kabui |
| 2022-01-22 | generate network | Alexander Kabui |
| 2022-01-22 | generate ctl plots for each trait | Alexander Kabui |
| 2022-01-22 | fixes for ctl script:generate ctl ctl_significant json | Alexander Kabui |
| 2022-01-22 | bugfixes for script;create pheno and geno objects | Alexander Kabui |
| 2022-01-22 | generate lineplot | Alexander Kabui |
| 2022-01-22 | minor fix:read input data from json file | Alexander Kabui |
| 2022-01-22 | export json data | Alexander Kabui |
| 2022-01-22 | get significant interactions | Alexander Kabui |
| 2022-01-22 | perform the ctl scan | Alexander Kabui |
| 2022-01-22 | fetch genotypes and phenotype files | Alexander Kabui |
| 2022-01-22 | init script ctl analysis | Alexander Kabui |
| 2021-12-22 | Refactor wgcna (#63)...* add r as a gn3 input
* calculate powers from user input
* fix merge conflict | Alexander Kabui |
| 2021-11-11 | Merge branch 'main' into feature/add_rqtl_pairscan | zsloan |
| 2021-10-29 | Feature/biweight reimplementation (#47)...* 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 | Alexander Kabui |
| 2021-10-25 | minor fixes for sript enable annotations | Alexander Kabui |
| 2021-10-25 | script modification : add debug statements | Alexander Kabui |
| 2021-10-14 | Fixed when model is set to account for situations with no covariates | zsloan |
| 2021-10-14 | Incorporated Danny's code for calculating QTL main effects into rqtl_wrapper.R | zsloan |
| 2021-10-12 | Merge branch 'main' of https://github.com/genenetwork/genenetwork3 into bug/f... | zsloan |
| 2021-10-12 | Merge branch 'main' of https://github.com/genenetwork/genenetwork3 into featu... | zsloan |
| 2021-09-27 | remove unnecessary comments and variables | Alexander Kabui |
| 2021-09-23 | Updated rqtl_wrapper to also return a map file when doing a pair-scan (since ... | zsloan |
| 2021-09-23 | Added line priting pair-scan results to CSV and changed the default step-size... | zsloan |
| 2021-09-23 | - Added scan_func function that determines whether scanone or scantwo...(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
| zsloan |
| 2021-09-23 | Added option for running pairscan to rqtl_wrapper.R | zsloan |
