(define-module (gn runner gemma)
  #:use-module (json)
  #:use-module (gn data genotype)
  #: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 (
            run-gemma
            ))

(define (run-gemma population data-id name trait-name traits)
  (define bxd-inds (geno-inds-bxd "BXD.json"))
  (assert (= 235 (length bxd-inds)))
  (if name
      (display (string-append "WE HAVE OUR BXD DATASET " name " and trait " trait-name " for precompute!\n")))
  (display data-id)
  (display traits)
  (newline)
  ;; ---- write phenotype file
  (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"))]
    (call-with-output-file pheno-fn
      (lambda (port)
        (for-each (lambda (ind)
                    (begin
                      (let* [(value (assoc-ref traits ind))
                             (outvalue (if value
                                           value
                                           "NA"))]
                        (display outvalue)
                        (newline)
                        (display outvalue port)
                        (newline port))))
                  bxd-inds)))

    ;; set up with ./.guix-shell -- guile -L . -s ./scripts/precompute/precompute-hits.scm

    ;; ---- 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 --debug --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 --population \"" population "\" --name \"" name "\" --trait \"" trait-name "\" --verbose --loco --json --debug --parallel --input " k-json-fn " -- -g BXD.8_geno.txt.gz -p " pheno-fn " -a BXD.8_snps.txt -lmm 2 -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)
    )
  )