Write gemma trait values (pheno file)

1 files changed, 28 insertions, 0 deletions

diff --git a/gn/data/dataset.scm b/gn/data/dataset.scm
index c21a663..f099171 100644
--- a/gn/data/dataset.scm
+++ b/gn/data/dataset.scm
@@ -7,15 +7,18 @@
   #:use-module (srfi srfi-1)
   #:use-module (dbi dbi)
   #:use-module (gn db mysql)
+  #:use-module (gn data genotype)
   #:use-module (gn data group)
   #:use-module (gn util convert)
   #:use-module (web gn-uri)
+  #:use-module (rnrs base) ; for assert
 
   #:export (
             dataset-name
             get-bxd-publish-list
             get-bxd-publish-values-list
             get-bxd-publish-name-value-dict
+            write-pheno-file
             ))
 
 (define (get-dataset db probesetfreeze-id)
@@ -68,3 +71,28 @@
                                                `(,(assoc-ref r "Name") . ,(assoc-ref r "value"))
                                                ) '())))
            )))))
+
+
+(define (write-pheno-file fn traits)
+  (define bxd-inds (geno-inds-bxd (pk "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"))]
+             (if value
+                 (begin
+                   (format #t "~s ~s" ind outvalue)
+                   (newline)))
+             (display outvalue port)
+             (newline port))))
+       bxd-inds)
+      (close port)
+      ))
+)