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;;; 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 "1.3.1")
(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
"0vll55v8wjc0179n5q9ch9ah3dvgymc374wlbz33yzyi35yr8ds2"))))
(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 hsmice-wrangled-gexp
(let ((script-profile (profile
(content (packages->manifest
(list gzip tar r r-dplyr r-genio
r-purrr r-readr r-tibble r-tidyr))))))
(with-imported-modules '((guix build utils))
#~(begin
(use-modules (guix build utils))
(mkdir #$output)
(set-path-environment-variable
"PATH" '("bin") '(#$script-profile))
(set-path-environment-variable
"R_LIBS_SITE" '("site-library") '(#$script-profile))
(invoke "tar" "-xvf" #$hsmice-data
"./HSmice/1_QTL_data/")
(invoke "Rscript"
#$(local-file "../e2e-tests/hsmice/wrangle.r")
"HSmice/1_QTL_data" #$output)))))
(define hsmice-wrangled
(computed-file "hsmice-wrangled" hsmice-wrangled-gexp))
(define hsmice-ciphertext-gexp
(let ((script-profile (profile
(content (packages->manifest (list pyhegp))))))
(with-imported-modules '((guix build utils))
#~(begin
(use-modules (guix build utils)
(srfi srfi-26))
(mkdir #$output)
(set-path-environment-variable
"PATH" '("bin") '(#$script-profile))
(for-each (cut install-file <> (getcwd))
(find-files #$hsmice-wrangled "\\.tsv$"))
;; Simple data sharing workflow
(invoke "pyhegp" "encrypt" "genotype.tsv" "phenotype.tsv")
;; Joint/federated analysis workflow
(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")
(for-each (cut install-file <> #$output)
(find-files (getcwd) "\\.tsv.hegp$"))))))
(define hsmice-ciphertext
(computed-file "hsmice-ciphertext" hsmice-ciphertext-gexp))
(define hsmice-r-mixed-model-gwas-gexp
(let ((gwas-script (local-file "../e2e-tests/hsmice/gwas.r"))
(script-profile (profile
(content (packages->manifest
(list r r-dplyr r-mixed-model-gwas
r-qqman r-readr r-stringr
r-tibble r-tidyr))))))
(with-imported-modules '((guix build utils))
#~(begin
(use-modules (guix build utils))
(mkdir #$output)
(set-path-environment-variable
"PATH" '("bin") '(#$script-profile))
(set-path-environment-variable
"R_LIBS_SITE" '("site-library") '(#$script-profile))
;; GWAS on plaintext
(invoke "Rscript" #$gwas-script
#$(file-append hsmice-wrangled "/genotype.tsv")
#$(file-append hsmice-wrangled "/phenotype.tsv")
(string-append #$output "/plaintext-pvalues"))
(copy-file "Rplots.pdf" (string-append #$output "/plaintext-manhattan.pdf"))
;; GWAS with simple ciphertext data sharing
(invoke "Rscript" #$gwas-script
#$(file-append hsmice-ciphertext "/genotype.tsv.hegp")
#$(file-append hsmice-ciphertext "/phenotype.tsv.hegp")
(string-append #$output "/ciphertext-pvalues"))
(copy-file "Rplots.pdf"
(string-append #$output "/ciphertext-manhattan.pdf"))
;; Joint federated GWAS
(invoke "Rscript" #$gwas-script
#$(file-append hsmice-ciphertext "/complete-genotype.tsv.hegp")
#$(file-append hsmice-ciphertext "/complete-phenotype.tsv.hegp")
(string-append #$output "/federated-ciphertext-pvalues"))
(copy-file "Rplots.pdf"
(string-append #$output "/federated-ciphertext-manhattan.pdf"))))))
(define hsmice-r-mixed-model-gwas
(computed-file "hsmice-r-mixed-model-gwas" hsmice-r-mixed-model-gwas-gexp))
(define hsmice-qtl-checked-gexp
(let ((script-profile (profile
(content (packages->manifest
(list python python-pandas))))))
(with-imported-modules '((guix build utils))
#~(begin
(use-modules (guix build utils)
(srfi srfi-26))
(mkdir #$output)
(set-path-environment-variable
"PATH" '("bin") '(#$script-profile))
(set-path-environment-variable
"GUIX_PYTHONPATH"
'(#$(string-append "lib/python"
(version-major+minor (package-version python))
"/site-packages"))
'(#$script-profile))
;; Check that the QTL is where it should be.
(for-each (cut invoke
"python3"
#$(local-file "../e2e-tests/hsmice/check-qtl.py")
<>)
(find-files #$hsmice-r-mixed-model-gwas
"\\-pvalues$"))))))
(define hsmice-qtl-checked
(computed-file "hsmice-qtl-checked" hsmice-qtl-checked-gexp))
(define-public hsmice-test
(directory-union "hsmice-test"
(list hsmice-r-mixed-model-gwas
hsmice-qtl-checked)))
hsmice-test
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