Allow custom name for IID columns by ofrei · Pull Request #123 · comorment/containers

ofrei · 2023-02-07T08:26:09Z

Fixes #21

Changes proposed in this pull request:

Before submitting

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I've updated or added any relevant docstrings following the syntax described in the
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If this PR fixes a bug, I've added a test that will fail without my fix.
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….dict file)

…fix21

ofrei · 2023-02-08T10:05:25Z

I'll address linter issues on a separate PR

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

espenhgn · 2023-04-25T16:48:13Z

@ofrei, please delete branch https://github.com/comorment/containers/tree/fix21 if it's no longer needed.

* 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

ofrei and others added 9 commits January 31, 2023 10:13

clarify comments

4516236

allow IID column in .pheno file to have a custom name (as defined in …

2fa7c95

….dict file)

fix rename_iid_column

6ce7e30

clarify comments

cd0f271

allow IID column in .pheno file to have a custom name (as defined in …

314e3c6

….dict file)

fix rename_iid_column

5a9f675

Merge branch 'fix21' of https://github.com/comorment/containers into …

4b8c31a

…fix21

add tests for identical FIDs and custom IIDs

3b2644a

also rename pheno.dict iid_column_name

0920ec0

ttfiliz force-pushed the fix21 branch from 6a0941e to 0920ec0 Compare February 7, 2023 08:47

ofrei marked this pull request as ready for review February 8, 2023 10:04

ofrei merged commit 92fc902 into main Feb 8, 2023

espenhgn deleted the fix21 branch June 25, 2024 12:27

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Allow custom name for IID columns #123

Allow custom name for IID columns #123
ofrei merged 9 commits intomainfrom
fix21

ofrei commented Feb 7, 2023

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ofrei commented Feb 8, 2023

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espenhgn commented Apr 25, 2023

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ofrei commented Feb 7, 2023

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ofrei commented Feb 8, 2023

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