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Diffstat (limited to '.guix/hsmice-test.scm')
| -rw-r--r-- | .guix/hsmice-test.scm | 148 |
1 files changed, 148 insertions, 0 deletions
diff --git a/.guix/hsmice-test.scm b/.guix/hsmice-test.scm new file mode 100644 index 0000000..ee8ecbd --- /dev/null +++ b/.guix/hsmice-test.scm @@ -0,0 +1,148 @@ +;;; pyhegp --- Homomorphic encryption of genotypes and phenotypes +;;; Copyright © 2025 Arun Isaac <arunisaac@systemreboot.net> +;;; +;;; This file is part of pyhegp. +;;; +;;; pyhegp is free software: you can redistribute it and/or modify it +;;; under the terms of the GNU General Public License as published by +;;; the Free Software Foundation, either version 3 of the License, or +;;; (at your option) any later version. +;;; +;;; pyhegp is distributed in the hope that it will be useful, but +;;; WITHOUT ANY WARRANTY; without even the implied warranty of +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +;;; General Public License for more details. +;;; +;;; You should have received a copy of the GNU General Public License +;;; along with pyhegp. If not, see <https://www.gnu.org/licenses/>. + +(define-module (hsmice-test) + #:use-module ((gn packages bioinformatics) #:select (r-genio)) + #:use-module ((gnu packages base) #:select (tar)) + #:use-module ((gnu packages compression) #:select (gzip)) + #:use-module ((gnu packages cran) #:select (r-dplyr r-purrr r-qqman r-stringr)) + #:use-module ((gnu packages python) #:select (python)) + #:use-module ((gnu packages python-science) #:select (python-pandas)) + #:use-module ((gnu packages python-xyz) #:select (python-click)) + #:use-module ((gnu packages statistics) #:select (r r-readr r-tibble r-tidyr)) + #:use-module (guix build-system r) + #:use-module (guix download) + #:use-module (guix gexp) + #:use-module (guix git-download) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix packages) + #:use-module (guix profiles) + #:use-module (guix utils) + #:use-module ((pyhegp-package) #:select (pyhegp))) + +;; See details of dataset at +;; https://rdr.ucl.ac.uk/articles/dataset/HSmice_tar_gz/24114471?file=42304248 +(define hsmice-data + (origin + (method url-fetch) + (uri "https://ndownloader.figshare.com/files/42304248") + (file-name "HSmice.tar.gz") + (sha256 + (base32 + "1s6a83r0mll8z2lfv1b94zr2sjdrky5nyq1mpgl8fjjb5s8v2vyx")))) + +(define-public r-mixed-model-gwas + (package + (name "r-mixed-model-gwas") + (version "1.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/encryption4genetics/mixed-model-gwas") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0yv86mw9m981vzl80j100lg05kc6jm5ijhq9b8zcd8f2lr3115db")))) + (build-system r-build-system) + (home-page "https://github.com/encryption4genetics/mixed-model-gwas") + (synopsis "R mixed model GWAS") + (description "@code{r-mixed-model-gwas} implements a mixed model @acronym{GWAS, +genome-wide association study} library for R.") + (license license:gpl3+))) + +(define test-profile + (profile + (content (packages->manifest (list gzip tar pyhegp + python python-click python-pandas + r r-dplyr r-genio + r-mixed-model-gwas r-purrr + r-qqman r-readr r-stringr + r-tibble r-tidyr))))) + +(define wrangle-script + (local-file "../e2e-tests/hsmice/wrangle.r")) + +(define gwas-script + (local-file "../e2e-tests/hsmice/gwas.r")) + +(define check-qtl-script + (local-file "../e2e-tests/hsmice/check-qtl.py")) + +(define hsmice-test-gexp + (with-imported-modules '((guix build utils)) + #~(begin + (use-modules (guix build utils)) + + (mkdir #$output) + (set-path-environment-variable + "PATH" '("/bin") '(#$test-profile)) + (set-path-environment-variable + "GUIX_PYTHONPATH" + '(#$(string-append "/lib/python" + (version-major+minor (package-version python)) + "/site-packages")) + '(#$test-profile)) + (set-path-environment-variable + "R_LIBS_SITE" '("/site-library") '(#$test-profile)) + (invoke "tar" "-xvf" #$hsmice-data + "./HSmice/1_QTL_data/") + (invoke "Rscript" #$wrangle-script "HSmice/1_QTL_data" ".") + + ;; GWAS on plaintext + (invoke "Rscript" #$gwas-script + "genotype.tsv" "phenotype.tsv" + (string-append #$output "/plaintext-pvalues")) + (copy-file "Rplots.pdf" (string-append #$output "/plaintext-manhattan.pdf")) + + ;; GWAS with simple ciphertext data sharing + (invoke "pyhegp" "encrypt" "genotype.tsv" "phenotype.tsv") + (invoke "Rscript" #$gwas-script + "genotype.tsv.hegp" "phenotype.tsv.hegp" + (string-append #$output "/ciphertext-pvalues")) + (copy-file "Rplots.pdf" + (string-append #$output "/ciphertext-manhattan.pdf")) + + ;; Joint federated GWAS + (invoke "pyhegp" "summary" "genotype1.tsv" "-o" "summary1") + (invoke "pyhegp" "summary" "genotype2.tsv" "-o" "summary2") + (invoke "pyhegp" "pool" "-o" "complete-summary" "summary1" "summary2") + (invoke "pyhegp" "encrypt" "-s" "complete-summary" "genotype1.tsv" "phenotype1.tsv") + (invoke "pyhegp" "encrypt" "-s" "complete-summary" "genotype2.tsv" "phenotype2.tsv") + (invoke "pyhegp" "cat-genotype" "-o" "complete-genotype.tsv.hegp" + "genotype1.tsv.hegp" "genotype2.tsv.hegp") + (invoke "pyhegp" "cat-phenotype" "-o" "complete-phenotype.tsv.hegp" + "phenotype1.tsv.hegp" "phenotype2.tsv.hegp") + (invoke "Rscript" #$gwas-script + "complete-genotype.tsv.hegp" "complete-phenotype.tsv.hegp" + (string-append #$output "/federated-ciphertext-pvalues")) + (copy-file "Rplots.pdf" + (string-append #$output "/federated-ciphertext-manhattan.pdf")) + + ;; Check that the QTL is where it should be. + (for-each (lambda (pvalues-file) + (invoke "python3" #$check-qtl-script + (string-append #$output "/" pvalues-file))) + (list "plaintext-pvalues" + "ciphertext-pvalues" + "federated-ciphertext-pvalues"))))) + +(define-public hsmice-test + (computed-file "hsmice-test" hsmice-test-gexp)) + +hsmice-test |