From fb22ae84c143a27ddc4699327e8aff6c93a0bf6c Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Fri, 24 Nov 2023 09:07:55 +0100
Subject: Fetch genotype inds from json file

---
 .gitignore                             |  1 +
 .guix-shell                            |  2 +-
 gn/data/genotype.scm                   | 23 +++++++++++++++++++++++
 gn/runner/gemma.scm                    |  9 ++++++---
 scripts/precompute/precompute-hits.scm |  6 ++++++
 5 files changed, 37 insertions(+), 4 deletions(-)
 create mode 100644 .gitignore
 create mode 100644 gn/data/genotype.scm

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..047b170
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1 @@
+BXD.*
diff --git a/.guix-shell b/.guix-shell
index 9f5b009..988e529 100755
--- a/.guix-shell
+++ b/.guix-shell
@@ -4,4 +4,4 @@
 
 echo "Create a shell to run tools. In the container"
 
-guix shell -C -F --network coreutils guile guile-dbi guile-dbd-mysql guile-fibers guile-json guile-gnutls guile-readline guile-redis openssl nss-certs gemma $*
+guix shell -C -D -F --network coreutils guile guile-dbi guile-dbd-mysql guile-fibers guile-json guile-gnutls guile-readline guile-redis openssl nss-certs gemma $*
diff --git a/gn/data/genotype.scm b/gn/data/genotype.scm
new file mode 100644
index 0000000..c7cb63c
--- /dev/null
+++ b/gn/data/genotype.scm
@@ -0,0 +1,23 @@
+(define-module (gn data genotype)
+  #:use-module (json)
+  #: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 (gn db sparql)
+  #:use-module (dbi dbi)
+  #:use-module (gn db mysql)
+  #:use-module (gn data group)
+  #:use-module (gn util convert)
+
+  #:export (
+            geno-inds-bxd
+            ))
+
+(define (geno-inds-bxd fn)
+  (let [(js (call-with-input-file fn
+              (lambda (port)
+                (json->scm port))))]
+    (vector->list (assoc-ref (car (vector->list (assoc-ref js "genofile"))) "sample_list"))
+))
diff --git a/gn/runner/gemma.scm b/gn/runner/gemma.scm
index 31a14f7..d9e43eb 100644
--- a/gn/runner/gemma.scm
+++ b/gn/runner/gemma.scm
@@ -17,13 +17,16 @@
   (display traits)
   (newline)
   ;; ---- write phenotype file
-  (call-with-output-file "test.tmp"
+  (call-with-output-file "pheno.txt"
     (lambda (port)
       (write 12 port)
       (newline port)
       (write "HELLO" port)
       ))
+  ;; set up with ./.guix-shell -- guile -L . -s ./scripts/precompute/precompute-hits.scm
 
-  ;; ---- start GEMMA precompute
-  (system "gemma")
+  ;; ---- to start GEMMA precompute inside container
+  ;; env LD_LIBRARY_PATH=$GUIX_ENVIRONMENT/lib/ guile -L . -s ./scripts/precompute/precompute-hits.scm
+  ;; --- First we compute K
+  (system (string-append "env GEMMA_COMMAND=/gemma/bin/gemma /gemma-wrapper/bin/gemma-wrapper --debug -- -gk -g BXD.8_geno.txt.gz -p pheno.txt -a BXD.8_snps.txt"  ))
   )
diff --git a/scripts/precompute/precompute-hits.scm b/scripts/precompute/precompute-hits.scm
index 0bce8d7..e8ba0a2 100755
--- a/scripts/precompute/precompute-hits.scm
+++ b/scripts/precompute/precompute-hits.scm
@@ -7,6 +7,7 @@
 (use-modules (dbi dbi)
              (gn db mysql)
              (gn data dataset)
+             (gn data genotype)
              (gn data hits)
              (gn data strains)
              (gn util convert)
@@ -16,6 +17,11 @@
              (srfi srfi-1)
              )
 
+
+(define inds (geno-inds-bxd "BXD.json"))
+(display inds)
+(assert (= 235 (length inds)))
+
 ;; potentially you want to test connection with mysql client:
 ;;
 ;;    mysql -uwebqtlout -pwebqtlout -A -h 127.0.0.1 -P 3306 db_webqtl -e "show tables;"
-- 
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