From 186da1d636f88421d1bbca0033e2d99a3b15e6cd Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Fri, 24 Nov 2023 09:43:17 +0100
Subject: Handle genotypes in gemma module

---
 gn/runner/gemma.scm                    | 4 ++++
 scripts/precompute/precompute-hits.scm | 4 ----
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/gn/runner/gemma.scm b/gn/runner/gemma.scm
index d9e43eb..67dae54 100644
--- a/gn/runner/gemma.scm
+++ b/gn/runner/gemma.scm
@@ -1,16 +1,20 @@
 (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 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)
diff --git a/scripts/precompute/precompute-hits.scm b/scripts/precompute/precompute-hits.scm
index e8ba0a2..b9dd746 100755
--- a/scripts/precompute/precompute-hits.scm
+++ b/scripts/precompute/precompute-hits.scm
@@ -7,7 +7,6 @@
 (use-modules (dbi dbi)
              (gn db mysql)
              (gn data dataset)
-             (gn data genotype)
              (gn data hits)
              (gn data strains)
              (gn util convert)
@@ -18,9 +17,6 @@
              )
 
 
-(define inds (geno-inds-bxd "BXD.json"))
-(display inds)
-(assert (= 235 (length inds)))
 
 ;; potentially you want to test connection with mysql client:
 ;;
-- 
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