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authorPjotr Prins2024-06-26 04:45:13 -0500
committerPjotr Prins2024-06-26 04:45:13 -0500
commite4775ccc0c24351e1ee428cddb0f320022509137 (patch)
tree868406d4c55b988a46bbd97e4c7fda543dcd2bc0 /gn/runner/gemma.scm
parent41735d8fbf4fbd0d137224f25b20cda6556ad484 (diff)
downloadgn-guile-e4775ccc0c24351e1ee428cddb0f320022509137.tar.gz
Read pheno JSON file and write out pheno file for gemma
Diffstat (limited to 'gn/runner/gemma.scm')
-rw-r--r--gn/runner/gemma.scm43
1 files changed, 23 insertions, 20 deletions
diff --git a/gn/runner/gemma.scm b/gn/runner/gemma.scm
index 131284a..4c1c374 100644
--- a/gn/runner/gemma.scm
+++ b/gn/runner/gemma.scm
@@ -10,16 +10,37 @@
#:use-module (rnrs base)
#:export (
+ write-pheno-file
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"))]
+ (format #t "~s ~s" ind outvalue)
+ (newline)
+ (display outvalue port)
+ (newline port))))
+ bxd-inds)
+ (close port)
+ ))
+)
+
(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 bxd-inds (geno-inds-bxd "BXD.json"))
(define ids (string-append (int-to-string data-id) ","
(int-to-string probeset-id) ","
(int-to-string probesetfreeze-id)))
- (assert (= 235 (length bxd-inds)))
(if name
(display (string-append "WE HAVE OUR " population " DATASET " name " and trait " trait-name " for precompute!\n")))
(display ids)
@@ -31,24 +52,6 @@
(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)
- (close port)
- ))
-
- ;; 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