unit tests for gwas.py by ttfiliz · Pull Request #119 · comorment/containers

ttfiliz · 2023-01-16T14:37:54Z

Fixes #116

Changes proposed in this pull request:

Added unit tests for gwas.py based on the use case gwas_demo

Before submitting

I've read and followed all steps in the Making a pull request
section of the CONTRIBUTING docs.
I've updated or added any relevant docstrings following the syntax described in the
Writing docstrings section of the CONTRIBUTING docs.
If this PR fixes a bug, I've added a test that will fail without my fix.
If this PR adds a new feature, I've added tests that sufficiently cover my new functionality.

espenhgn

Thanks @ttfiliz . I'm getting some test errors with this as/REF/ dir doesn't exist from within the container w. py.test -v tests/test_gwas_py.py.

...
Traceback (most recent call last):
  File "/tmp/tmpxw0lxn6n/gwas.py", line 1005, in <module>
    args.func(args, log)
  File "/tmp/tmpxw0lxn6n/gwas.py", line 625, in execute_gwas
    fix_and_validate_pheno_args(args, log)
  File "/tmp/tmpxw0lxn6n/gwas.py", line 224, in fix_and_validate_pheno_args
    check_input_file(args.fam)
  File "/tmp/tmpxw0lxn6n/gwas.py", line 823, in check_input_file
    raise ValueError("Input file does not exist: {f}".format(f=fname))
ValueError: Input file does not exist: /REF/examples/regenie/example_3chr.fam
...

Can you make sure that you don't have host environment variables like SINGULARITY_BIND in effect? Setting this at the Python level explicitly within the test script ought to do I believe(os.environ["SINGULARITY_BIND"] = ...)

espenhgn

Thanks, think this is now good to go!

tests/test_gwas_py.py

…ix116

espenhgn · 2023-01-18T10:39:04Z

@ofrei, can you merge this? I'm fine with it. All tests pass on my end.

commit 2dd1c58 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Fri Feb 17 07:28:28 2023 +0000 updated md5sum commit 6ceaaf5 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Fri Feb 17 07:26:21 2023 +0000 rebuild r.sif container commit 021e333 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Fri Feb 17 07:23:52 2023 +0000 +PRSice_linux, revise R package repo commit b984ff6 Merge: 3666140 99d7c0e Author: deepchocolate <andreas@systerdyster.se> Date: Fri Feb 10 15:33:25 2023 +0100 Merge branch 'deepchocolate/ldpred2_ld' commit 99d7c0e Author: deepchocolate <andreas@systerdyster.se> Date: Fri Feb 10 13:50:16 2023 +0100 Added note on filtering commit f4f7e06 Author: deepchocolate <andreas@systerdyster.se> Date: Fri Feb 10 13:40:51 2023 +0100 Renamed --file-keep-snps to --extract commit 27413a6 Author: deepchocolate <andreas@systerdyster.se> Date: Fri Feb 10 13:27:51 2023 +0100 Removed --sumstats-sep from test script commit a94a18a Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Fri Feb 10 10:12:33 2023 +0000 removed redundant --sumstats-sep arg commit 3666140 Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Thu Feb 9 22:57:39 2023 +0100 fix flake8 for combine_figures.py commit f8f904e Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Thu Feb 9 22:54:05 2023 +0100 noqa: W605 commit 5e3ff1d Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Thu Feb 9 22:51:45 2023 +0100 manually edit to clear most errors commit c89ac5b Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Thu Feb 9 21:56:37 2023 +0100 autopep8 --max-line-length 119 --ignore E302 commit 246ad6b Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Thu Feb 9 23:01:35 2023 +0100 update config for flake8 linter (#126) * test flake8_args * Node.js 12 actions are deprecated * nonsensical edit that should trigger E501 * flake8_args * bad style * check if flake8 is reporting * check E302 nontrigger * check E302 nontrigger * revert things * revert gwas.py * updated changelog commit 8f0f2b5 Author: deepchocolate <andreas@systerdyster.se> Date: Thu Feb 9 16:04:15 2023 +0100 Added threshold filtering parameter commit 92fc902 Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Wed Feb 8 11:05:04 2023 +0100 Allow custom name for IID columns (#123) * clarify comments * allow IID column in .pheno file to have a custom name (as defined in .dict file) * fix rename_iid_column * clarify comments * allow IID column in .pheno file to have a custom name (as defined in .dict file) * fix rename_iid_column * add tests for identical FIDs and custom IIDs * also rename pheno.dict iid_column_name --------- Co-authored-by: ttfiliz <110425985+ttfiliz@users.noreply.github.com> commit 814db96 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Wed Feb 1 14:52:05 2023 +0000 some markdown stuff commit 05f520f Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Wed Feb 1 10:57:38 2023 +0000 sensible score values. Use plink from container commit e653381 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Wed Feb 1 10:42:39 2023 +0000 add --sumstats-sep option etc. commit 5673a1f Author: ttfiliz <110425985+ttfiliz@users.noreply.github.com> Date: Tue Jan 31 09:58:49 2023 +0100 throw an error if --variance-standardize is applied to a continuous variable without variation (#121) commit e70c033 Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 31 09:47:58 2023 +0100 Updated changelog commit 9ece1f8 Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 31 09:47:38 2023 +0100 Updated LDpred2 README commit 6e06f24 Author: deepchocolate <andreas@systerdyster.se> Date: Thu Jan 26 17:55:33 2023 +0100 Renamed --geno-file argument commit 00e8d35 Author: deepchocolate <andreas@systerdyster.se> Date: Thu Jan 26 13:56:02 2023 +0100 Added readme in folder for testdata commit b6da1a3 Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 24 13:22:59 2023 +0100 Added auto mode to tests commit 7c1bbf4 Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Tue Jan 24 09:11:15 2023 +0100 Update README.md commit 0bb5f1a Author: ttfiliz <110425985+ttfiliz@users.noreply.github.com> Date: Tue Jan 24 09:06:18 2023 +0100 unit tests for gwas.py (#119) * Added unit tests for gwas.py * change cwd back to original cwd after each test * updated changelog * set environment variables in test script * Update README.md * removed unnecessary singularity bind path * update README.md Co-authored-by: Espen Hagen <2492641+espenhgn@users.noreply.github.com> commit 31036f8 Author: deepchocolate <andreas@systerdyster.se> Date: Wed Jan 11 15:22:51 2023 +0100 Added sampling of individuals commit bb8f80d Author: deepchocolate <andreas@systerdyster.se> Date: Wed Jan 11 14:45:18 2023 +0100 Removed redundant code, fixed chr2use argument commit ea54fff Author: deepchocolate <andreas@systerdyster.se> Date: Wed Jan 11 14:26:07 2023 +0100 Cleanup, fixed arguments to --sumstats commit 82d39c1 Author: deepchocolate <andreas@systerdyster.se> Date: Wed Jan 11 14:25:35 2023 +0100 Reorganized tests commit 896eadf Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 10 20:39:57 2023 +0100 Added test runs commit 304f19a Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 10 17:24:22 2023 +0100 Working version commit 6b47b30 Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 10 10:55:55 2023 +0100 Added test runs commit 087d50f Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 10 10:55:25 2023 +0100 Trimmed some output

commit 4f7a26a Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Mon Feb 20 09:29:28 2023 +0000 added pROC library commit 2dd1c58 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Fri Feb 17 07:28:28 2023 +0000 updated md5sum commit 6ceaaf5 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Fri Feb 17 07:26:21 2023 +0000 rebuild r.sif container commit 021e333 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Fri Feb 17 07:23:52 2023 +0000 +PRSice_linux, revise R package repo commit b984ff6 Merge: 3666140 99d7c0e Author: deepchocolate <andreas@systerdyster.se> Date: Fri Feb 10 15:33:25 2023 +0100 Merge branch 'deepchocolate/ldpred2_ld' commit 99d7c0e Author: deepchocolate <andreas@systerdyster.se> Date: Fri Feb 10 13:50:16 2023 +0100 Added note on filtering commit f4f7e06 Author: deepchocolate <andreas@systerdyster.se> Date: Fri Feb 10 13:40:51 2023 +0100 Renamed --file-keep-snps to --extract commit 27413a6 Author: deepchocolate <andreas@systerdyster.se> Date: Fri Feb 10 13:27:51 2023 +0100 Removed --sumstats-sep from test script commit a94a18a Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Fri Feb 10 10:12:33 2023 +0000 removed redundant --sumstats-sep arg commit 3666140 Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Thu Feb 9 22:57:39 2023 +0100 fix flake8 for combine_figures.py commit f8f904e Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Thu Feb 9 22:54:05 2023 +0100 noqa: W605 commit 5e3ff1d Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Thu Feb 9 22:51:45 2023 +0100 manually edit to clear most errors commit c89ac5b Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Thu Feb 9 21:56:37 2023 +0100 autopep8 --max-line-length 119 --ignore E302 commit 246ad6b Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Thu Feb 9 23:01:35 2023 +0100 update config for flake8 linter (#126) * test flake8_args * Node.js 12 actions are deprecated * nonsensical edit that should trigger E501 * flake8_args * bad style * check if flake8 is reporting * check E302 nontrigger * check E302 nontrigger * revert things * revert gwas.py * updated changelog commit 8f0f2b5 Author: deepchocolate <andreas@systerdyster.se> Date: Thu Feb 9 16:04:15 2023 +0100 Added threshold filtering parameter commit 92fc902 Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Wed Feb 8 11:05:04 2023 +0100 Allow custom name for IID columns (#123) * clarify comments * allow IID column in .pheno file to have a custom name (as defined in .dict file) * fix rename_iid_column * clarify comments * allow IID column in .pheno file to have a custom name (as defined in .dict file) * fix rename_iid_column * add tests for identical FIDs and custom IIDs * also rename pheno.dict iid_column_name --------- Co-authored-by: ttfiliz <110425985+ttfiliz@users.noreply.github.com> commit 814db96 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Wed Feb 1 14:52:05 2023 +0000 some markdown stuff commit 05f520f Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Wed Feb 1 10:57:38 2023 +0000 sensible score values. Use plink from container commit e653381 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Wed Feb 1 10:42:39 2023 +0000 add --sumstats-sep option etc. commit 5673a1f Author: ttfiliz <110425985+ttfiliz@users.noreply.github.com> Date: Tue Jan 31 09:58:49 2023 +0100 throw an error if --variance-standardize is applied to a continuous variable without variation (#121) commit e70c033 Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 31 09:47:58 2023 +0100 Updated changelog commit 9ece1f8 Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 31 09:47:38 2023 +0100 Updated LDpred2 README commit 6e06f24 Author: deepchocolate <andreas@systerdyster.se> Date: Thu Jan 26 17:55:33 2023 +0100 Renamed --geno-file argument commit 00e8d35 Author: deepchocolate <andreas@systerdyster.se> Date: Thu Jan 26 13:56:02 2023 +0100 Added readme in folder for testdata commit b6da1a3 Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 24 13:22:59 2023 +0100 Added auto mode to tests commit 7c1bbf4 Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Tue Jan 24 09:11:15 2023 +0100 Update README.md commit 0bb5f1a Author: ttfiliz <110425985+ttfiliz@users.noreply.github.com> Date: Tue Jan 24 09:06:18 2023 +0100 unit tests for gwas.py (#119) * Added unit tests for gwas.py * change cwd back to original cwd after each test * updated changelog * set environment variables in test script * Update README.md * removed unnecessary singularity bind path * update README.md Co-authored-by: Espen Hagen <2492641+espenhgn@users.noreply.github.com> commit 31036f8 Author: deepchocolate <andreas@systerdyster.se> Date: Wed Jan 11 15:22:51 2023 +0100 Added sampling of individuals commit bb8f80d Author: deepchocolate <andreas@systerdyster.se> Date: Wed Jan 11 14:45:18 2023 +0100 Removed redundant code, fixed chr2use argument commit ea54fff Author: deepchocolate <andreas@systerdyster.se> Date: Wed Jan 11 14:26:07 2023 +0100 Cleanup, fixed arguments to --sumstats commit 82d39c1 Author: deepchocolate <andreas@systerdyster.se> Date: Wed Jan 11 14:25:35 2023 +0100 Reorganized tests commit 896eadf Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 10 20:39:57 2023 +0100 Added test runs commit 304f19a Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 10 17:24:22 2023 +0100 Working version commit 6b47b30 Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 10 10:55:55 2023 +0100 Added test runs commit 087d50f Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 10 10:55:25 2023 +0100 Trimmed some output

* install LDAK * W.I.P. * not implemented LDAK test * add missing .eigenvec file * add some R scripts * PGS using prsice2 * backup w.i.p. * backing up files * work in progress * work in progress * rebuild gwas.sif including ldak tool * rebuild r.sif with PRSice_linux binary * backup * hidden functions return strings * work in progress * Work in progress * w.i.p. * w.i.p. * w.i.p. * script updates + config.yaml file * w.i.p. * simplify notebook * w.i.p. * w.i.p. * linting * linting * linting * fuck * post_run using python container * add runtime script for interactive use * some flexibility w Eigenvec_file * add option for bash and slurm jobs * ldpred2.R script from main branch * BasePGRS->BasePGS * backin up * fixed application with synthetic data * cleanup * backing up * don't use log object from outer scope * fix parallelization * code that should run on TSD * remove Data_postfix arg in main classes * adapting PGS/pgs as common term * PRS -> PGS etc. * renamed file * updating pgs_exec w. example * some user example script updates * subparser added for method specific * updates to usage * Input_dir/Data_prefix to Geno_file * rebuilt container, tee build logs * linting * suppress some CI warnings * setup-python@v4 * add R script for evaluating model fit * make Phenotype mandatory arg * sep * df.merge stuff * backup * add some example on MoBa * fit lm model <pheno>~PGS+PC1+...+PCN+<cov> * move R scripts to Rscripts dir * write results to "results" * get rid of semiredundant kwargs * do not autoasses #cores * use env variables * fixes * disgusting * path things * chromosomes * minor formatting * w.i.p. * reformatting env setup * paths * clump and a2->a0 fixes * minifixes * Squashed commit of the following: commit 2dd1c58 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Fri Feb 17 07:28:28 2023 +0000 updated md5sum commit 6ceaaf5 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Fri Feb 17 07:26:21 2023 +0000 rebuild r.sif container commit 021e333 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Fri Feb 17 07:23:52 2023 +0000 +PRSice_linux, revise R package repo commit b984ff6 Merge: 3666140 99d7c0e Author: deepchocolate <andreas@systerdyster.se> Date: Fri Feb 10 15:33:25 2023 +0100 Merge branch 'deepchocolate/ldpred2_ld' commit 99d7c0e Author: deepchocolate <andreas@systerdyster.se> Date: Fri Feb 10 13:50:16 2023 +0100 Added note on filtering commit f4f7e06 Author: deepchocolate <andreas@systerdyster.se> Date: Fri Feb 10 13:40:51 2023 +0100 Renamed --file-keep-snps to --extract commit 27413a6 Author: deepchocolate <andreas@systerdyster.se> Date: Fri Feb 10 13:27:51 2023 +0100 Removed --sumstats-sep from test script commit a94a18a Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Fri Feb 10 10:12:33 2023 +0000 removed redundant --sumstats-sep arg commit 3666140 Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Thu Feb 9 22:57:39 2023 +0100 fix flake8 for combine_figures.py commit f8f904e Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Thu Feb 9 22:54:05 2023 +0100 noqa: W605 commit 5e3ff1d Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Thu Feb 9 22:51:45 2023 +0100 manually edit to clear most errors commit c89ac5b Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Thu Feb 9 21:56:37 2023 +0100 autopep8 --max-line-length 119 --ignore E302 commit 246ad6b Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Thu Feb 9 23:01:35 2023 +0100 update config for flake8 linter (#126) * test flake8_args * Node.js 12 actions are deprecated * nonsensical edit that should trigger E501 * flake8_args * bad style * check if flake8 is reporting * check E302 nontrigger * check E302 nontrigger * revert things * revert gwas.py * updated changelog commit 8f0f2b5 Author: deepchocolate <andreas@systerdyster.se> Date: Thu Feb 9 16:04:15 2023 +0100 Added threshold filtering parameter commit 92fc902 Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Wed Feb 8 11:05:04 2023 +0100 Allow custom name for IID columns (#123) * clarify comments * allow IID column in .pheno file to have a custom name (as defined in .dict file) * fix rename_iid_column * clarify comments * allow IID column in .pheno file to have a custom name (as defined in .dict file) * fix rename_iid_column * add tests for identical FIDs and custom IIDs * also rename pheno.dict iid_column_name --------- Co-authored-by: ttfiliz <110425985+ttfiliz@users.noreply.github.com> commit 814db96 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Wed Feb 1 14:52:05 2023 +0000 some markdown stuff commit 05f520f Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Wed Feb 1 10:57:38 2023 +0000 sensible score values. Use plink from container commit e653381 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Wed Feb 1 10:42:39 2023 +0000 add --sumstats-sep option etc. commit 5673a1f Author: ttfiliz <110425985+ttfiliz@users.noreply.github.com> Date: Tue Jan 31 09:58:49 2023 +0100 throw an error if --variance-standardize is applied to a continuous variable without variation (#121) commit e70c033 Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 31 09:47:58 2023 +0100 Updated changelog commit 9ece1f8 Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 31 09:47:38 2023 +0100 Updated LDpred2 README commit 6e06f24 Author: deepchocolate <andreas@systerdyster.se> Date: Thu Jan 26 17:55:33 2023 +0100 Renamed --geno-file argument commit 00e8d35 Author: deepchocolate <andreas@systerdyster.se> Date: Thu Jan 26 13:56:02 2023 +0100 Added readme in folder for testdata commit b6da1a3 Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 24 13:22:59 2023 +0100 Added auto mode to tests commit 7c1bbf4 Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Tue Jan 24 09:11:15 2023 +0100 Update README.md commit 0bb5f1a Author: ttfiliz <110425985+ttfiliz@users.noreply.github.com> Date: Tue Jan 24 09:06:18 2023 +0100 unit tests for gwas.py (#119) * Added unit tests for gwas.py * change cwd back to original cwd after each test * updated changelog * set environment variables in test script * Update README.md * removed unnecessary singularity bind path * update README.md Co-authored-by: Espen Hagen <2492641+espenhgn@users.noreply.github.com> commit 31036f8 Author: deepchocolate <andreas@systerdyster.se> Date: Wed Jan 11 15:22:51 2023 +0100 Added sampling of individuals commit bb8f80d Author: deepchocolate <andreas@systerdyster.se> Date: Wed Jan 11 14:45:18 2023 +0100 Removed redundant code, fixed chr2use argument commit ea54fff Author: deepchocolate <andreas@systerdyster.se> Date: Wed Jan 11 14:26:07 2023 +0100 Cleanup, fixed arguments to --sumstats commit 82d39c1 Author: deepchocolate <andreas@systerdyster.se> Date: Wed Jan 11 14:25:35 2023 +0100 Reorganized tests commit 896eadf Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 10 20:39:57 2023 +0100 Added test runs commit 304f19a Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 10 17:24:22 2023 +0100 Working version commit 6b47b30 Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 10 10:55:55 2023 +0100 Added test runs commit 087d50f Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 10 10:55:25 2023 +0100 Trimmed some output * revert gwas.py to main branch * multithreading * multithreading * fixes * fix action * Squashed commit of the following: commit 4f7a26a Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Mon Feb 20 09:29:28 2023 +0000 added pROC library commit 2dd1c58 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Fri Feb 17 07:28:28 2023 +0000 updated md5sum commit 6ceaaf5 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Fri Feb 17 07:26:21 2023 +0000 rebuild r.sif container commit 021e333 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Fri Feb 17 07:23:52 2023 +0000 +PRSice_linux, revise R package repo commit b984ff6 Merge: 3666140 99d7c0e Author: deepchocolate <andreas@systerdyster.se> Date: Fri Feb 10 15:33:25 2023 +0100 Merge branch 'deepchocolate/ldpred2_ld' commit 99d7c0e Author: deepchocolate <andreas@systerdyster.se> Date: Fri Feb 10 13:50:16 2023 +0100 Added note on filtering commit f4f7e06 Author: deepchocolate <andreas@systerdyster.se> Date: Fri Feb 10 13:40:51 2023 +0100 Renamed --file-keep-snps to --extract commit 27413a6 Author: deepchocolate <andreas@systerdyster.se> Date: Fri Feb 10 13:27:51 2023 +0100 Removed --sumstats-sep from test script commit a94a18a Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Fri Feb 10 10:12:33 2023 +0000 removed redundant --sumstats-sep arg commit 3666140 Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Thu Feb 9 22:57:39 2023 +0100 fix flake8 for combine_figures.py commit f8f904e Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Thu Feb 9 22:54:05 2023 +0100 noqa: W605 commit 5e3ff1d Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Thu Feb 9 22:51:45 2023 +0100 manually edit to clear most errors commit c89ac5b Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Thu Feb 9 21:56:37 2023 +0100 autopep8 --max-line-length 119 --ignore E302 commit 246ad6b Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Thu Feb 9 23:01:35 2023 +0100 update config for flake8 linter (#126) * test flake8_args * Node.js 12 actions are deprecated * nonsensical edit that should trigger E501 * flake8_args * bad style * check if flake8 is reporting * check E302 nontrigger * check E302 nontrigger * revert things * revert gwas.py * updated changelog commit 8f0f2b5 Author: deepchocolate <andreas@systerdyster.se> Date: Thu Feb 9 16:04:15 2023 +0100 Added threshold filtering parameter commit 92fc902 Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Wed Feb 8 11:05:04 2023 +0100 Allow custom name for IID columns (#123) * clarify comments * allow IID column in .pheno file to have a custom name (as defined in .dict file) * fix rename_iid_column * clarify comments * allow IID column in .pheno file to have a custom name (as defined in .dict file) * fix rename_iid_column * add tests for identical FIDs and custom IIDs * also rename pheno.dict iid_column_name --------- Co-authored-by: ttfiliz <110425985+ttfiliz@users.noreply.github.com> commit 814db96 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Wed Feb 1 14:52:05 2023 +0000 some markdown stuff commit 05f520f Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Wed Feb 1 10:57:38 2023 +0000 sensible score values. Use plink from container commit e653381 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Wed Feb 1 10:42:39 2023 +0000 add --sumstats-sep option etc. commit 5673a1f Author: ttfiliz <110425985+ttfiliz@users.noreply.github.com> Date: Tue Jan 31 09:58:49 2023 +0100 throw an error if --variance-standardize is applied to a continuous variable without variation (#121) commit e70c033 Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 31 09:47:58 2023 +0100 Updated changelog commit 9ece1f8 Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 31 09:47:38 2023 +0100 Updated LDpred2 README commit 6e06f24 Author: deepchocolate <andreas@systerdyster.se> Date: Thu Jan 26 17:55:33 2023 +0100 Renamed --geno-file argument commit 00e8d35 Author: deepchocolate <andreas@systerdyster.se> Date: Thu Jan 26 13:56:02 2023 +0100 Added readme in folder for testdata commit b6da1a3 Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 24 13:22:59 2023 +0100 Added auto mode to tests commit 7c1bbf4 Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Tue Jan 24 09:11:15 2023 +0100 Update README.md commit 0bb5f1a Author: ttfiliz <110425985+ttfiliz@users.noreply.github.com> Date: Tue Jan 24 09:06:18 2023 +0100 unit tests for gwas.py (#119) * Added unit tests for gwas.py * change cwd back to original cwd after each test * updated changelog * set environment variables in test script * Update README.md * removed unnecessary singularity bind path * update README.md Co-authored-by: Espen Hagen <2492641+espenhgn@users.noreply.github.com> commit 31036f8 Author: deepchocolate <andreas@systerdyster.se> Date: Wed Jan 11 15:22:51 2023 +0100 Added sampling of individuals commit bb8f80d Author: deepchocolate <andreas@systerdyster.se> Date: Wed Jan 11 14:45:18 2023 +0100 Removed redundant code, fixed chr2use argument commit ea54fff Author: deepchocolate <andreas@systerdyster.se> Date: Wed Jan 11 14:26:07 2023 +0100 Cleanup, fixed arguments to --sumstats commit 82d39c1 Author: deepchocolate <andreas@systerdyster.se> Date: Wed Jan 11 14:25:35 2023 +0100 Reorganized tests commit 896eadf Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 10 20:39:57 2023 +0100 Added test runs commit 304f19a Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 10 17:24:22 2023 +0100 Working version commit 6b47b30 Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 10 10:55:55 2023 +0100 Added test runs commit 087d50f Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 10 10:55:25 2023 +0100 Trimmed some output * ncores * split in two scripts * fixes * add clump_field parameter to PGS_plink * disable sorting while merging * remove use of --pheno-file and --col-pheno * fixes * notebooks * newline * added gtsummary r package * added R flextable * added R parameters * cleanup merge * better r lib test, PR cleanup * formatting * added R2 calcs * removed outdated ldpred2 files * renaming params * renaming variable nems etc. * clean up variable names * eigenvec file stuff * fixes * moving files * updated .gitignore * nPCs * cleanup * comment * misc updates * posit cran clone, new R libraries * fixing build * rebuilt r.sif container * linting * linting * add more R stuff * docs * plink score_args -> score_columns * cleanup * limit PLINK cpu usage * wrap up R packages * updated r.sif build procedure and scripts * update R build recipes and test * rebuilt r.sif * hadolint * better crash handling, explicit args w. createBackingFile.R * docs, deal with prsice2 bar-levels/fastscore * updated MoBa scripts * added lm/glm fits/stats w.o. covariates; ORs * details on output * string formatting * MplusAutomation/PredictABEL added to r.sif * rebuilt r.sif * roll back install_minimac4.sh script to main * removed non-lfs file (will re-add) * prep add EUR.eigenvec file * Add missing PRSice2 tutorial file * updated changelog w. main changes * github markdown math * typo * better math formatting w. sphinx * got rid of a myst-parser warning * flake8 fix * fixed broken test of createBackingFile.R

ttfiliz added 3 commits January 16, 2023 12:24

Added unit tests for gwas.py

86b7e3d

change cwd back to original cwd after each test

87fd8d6

updated changelog

2d28451

espenhgn self-requested a review January 17, 2023 09:11

espenhgn reviewed Jan 17, 2023

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set environment variables in test script

b6e957c

ttfiliz requested a review from espenhgn January 17, 2023 15:02

espenhgn added 2 commits January 18, 2023 10:05

Merge branch 'main' into fix116

7d05f32

Update README.md

8012a4f

espenhgn approved these changes Jan 18, 2023

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ofrei reviewed Jan 18, 2023

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tests/test_gwas_py.py Outdated Show resolved Hide resolved

ttfiliz added 3 commits January 18, 2023 09:33

removed unnecessary singularity bind path

e9ea7d2

Merge branch 'fix116' of https://github.com/ttfiliz/containers into f…

efefe7f

…ix116

update README.md

bb50904

ttfiliz merged commit 0bb5f1a into comorment:main Jan 24, 2023

ttfiliz deleted the fix116 branch March 11, 2024 08:26

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unit tests for gwas.py#119

unit tests for gwas.py#119
ttfiliz merged 9 commits intocomorment:mainfrom
ttfiliz:fix116

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ttfiliz commented Jan 16, 2023

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