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(define-module (gn runner gemma)
#:use-module (json)
#:use-module (gn data genotype)
#:use-module (gn util convert)
#:use-module (ice-9 match)
#:use-module (ice-9 format)
#:use-module (ice-9 iconv)
#:use-module (ice-9 receive)
#:use-module (ice-9 string-fun)
#:use-module (rnrs base)
#:export (
write-pheno-file
invoke-gemma-wrapper-loco
run-gemma
))
(define (write-pheno-file fn traits)
(define bxd-inds (geno-inds-bxd "BXD.json"))
(assert (= 235 (length bxd-inds)))
(display bxd-inds)
(call-with-output-file fn
(lambda (port)
(for-each
(lambda (ind)
(begin
(let* [(value (assoc-ref traits ind))
(outvalue (if value
value
"NA"))]
(if value
(begin
(format #t "~s ~s" ind outvalue)
(newline)))
(display outvalue port)
(newline port))))
bxd-inds)
(close port)
))
)
(define (invoke-gemma-wrapper-loco name trait-name trait-fn pheno-fn geno-fn)
"Create a tmpdir and invoke gemma-wrapper using parallel LOCO. Note that at this point we use a number of defaults for BXD"
(let* [(population "BXD")
(sys-tmpdir (getenv "TMPDIR"))
(tmpdir (mkdtemp (string-append sys-tmpdir "/run-gemma-XXXXXX")))
(k-json-fn (string-append tmpdir "/K.json"))
(gwa-json-fn (string-append tmpdir "/GWA.json"))
(trait-json-fn (string-append tmpdir "/" trait-fn))]
(copy-file trait-fn trait-json-fn)
;; --- First we compute K - control output goes to K.json
(let [(err (system (string-append "/gemma-wrapper/bin/gemma-wrapper --verbose --population \"" population "\" --name \"" name "\" --trait \"" trait-name "\" --verbose --loco --json --parallel -- -gk -g " geno-fn " -p " pheno-fn " -a BXD.8_snps.txt > " k-json-fn )))]
(if (not (= err 0))
(exit err)))
(let [(err (system (string-append "/gemma-wrapper/bin/gemma-wrapper --meta \"" trait-json-fn "\" --population \"" population "\" --name \"" name "\" --id \"" trait-name "\" --trait \"" trait-name "\" --verbose --loco --json --lmdb --input " k-json-fn " -- -g " geno-fn " -p " pheno-fn " -a BXD.8_snps.txt -lmm 9 -maf 0.1 > " gwa-json-fn)))]
(if (not (= err 0))
(exit err)))
(delete-file pheno-fn)
(delete-file gwa-json-fn)
(delete-file k-json-fn)
(delete-file trait-json-fn)
(rmdir tmpdir)
)
)
(define (run-gemma population data-id probeset-id probesetfreeze-id name trait-name traits)
"Run gemma-wrapper to compute GRM and GWA. On failure the run will stop(!)"
(define ids (string-append (int-to-string data-id) ","
(int-to-string probeset-id) ","
(int-to-string probesetfreeze-id)))
(if name
(display (string-append "WE HAVE OUR " population " DATASET " name " and trait " trait-name " for precompute!\n")))
(display ids)
(display traits)
(newline)
(let* [(sys-tmpdir (getenv "TMPDIR"))
(tmpdir (mkdtemp (string-append sys-tmpdir "/run-gemma-XXXXXX")))
(pheno-fn (string-append tmpdir "/pheno.txt"))
(k-json-fn (string-append tmpdir "/K.json"))
(gwa-json-fn (string-append tmpdir "/GWA.json"))]
;; ---- to start GEMMA precompute inside container
;; env TMPDIR=. LD_LIBRARY_PATH=$GUIX_ENVIRONMENT/lib/ guile -L . -s ./scripts/precompute/precompute-hits.scm
;; --- First we compute K - control output goes to K.json
(let [(err (system (string-append "env GEMMA_COMMAND=gemma /gemma-wrapper/bin/gemma-wrapper --population \"" population "\" --name \"" name "\" --trait \"" trait-name "\" --verbose --loco --json --parallel -- -gk -g BXD.8_geno.txt.gz -p " pheno-fn " -a BXD.8_snps.txt > " k-json-fn )))]
(if (not (= err 0))
(exit err)))
(let [(err (system (string-append "env GEMMA_COMMAND=gemma /gemma-wrapper/bin/gemma-wrapper --keep --population \"" population "\" --name \"" name "\" --id \"" ids "\" --trait \"" trait-name "\" --verbose --loco --json --parallel --input " k-json-fn " -- -g BXD.8_geno.txt.gz -p " pheno-fn " -a BXD.8_snps.txt -lmm 9 -maf 0.1 > " gwa-json-fn)))]
(if (not (= err 0))
(exit err)))
(delete-file pheno-fn)
(delete-file gwa-json-fn)
(delete-file k-json-fn)
(rmdir tmpdir)
)
#t
)
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