aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
-rw-r--r--.gitignore1
-rwxr-xr-x.guix-shell2
-rw-r--r--gn/data/genotype.scm23
-rw-r--r--gn/runner/gemma.scm9
-rwxr-xr-xscripts/precompute/precompute-hits.scm6
5 files changed, 37 insertions, 4 deletions
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;"