From 5600deccdd446cd8f1c287479051590236fb2959 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Thu, 4 Jan 2024 15:29:21 +0100
Subject: Use tmpfn for pheno output

---
 gn/runner/gemma.scm | 50 +++++++++++++++++++++++++++-----------------------
 1 file changed, 27 insertions(+), 23 deletions(-)

(limited to 'gn/runner')

diff --git a/gn/runner/gemma.scm b/gn/runner/gemma.scm
index d6b08f2..bcb4c36 100644
--- a/gn/runner/gemma.scm
+++ b/gn/runner/gemma.scm
@@ -21,28 +21,32 @@
   (display traits)
   (newline)
   ;; ---- write phenotype file
-  (call-with-output-file "pheno.txt"
-    (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)))
+  (let* [(port (mkstemp "pheno.txt-XXXXXX"))
+         (pheno-fn (port-filename 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
+    ;; set up with ./.guix-shell -- guile -L . -s ./scripts/precompute/precompute-hits.scm
 
-  ;; ---- to start GEMMA precompute inside container
-  ;; env TMPDIR=. LD_LIBRARY_PATH=$GUIX_ENVIRONMENT/lib/ guile -L . -s ./scripts/precompute/precompute-hits.scm
-  ;; --- First we compute K - control output goes to K.json
-  (let [(err (system (string-append "env GEMMA_COMMAND=gemma /gemma-wrapper/bin/gemma-wrapper --population \"" population "\" --name \"" name "\" --trait \"" trait-name "\" --verbose --loco --json --debug --parallel -- -gk -g BXD.8_geno.txt.gz -p pheno.txt -a BXD.8_snps.txt > K.json"  )))]
-    (if (not (= err 0))
-    (exit err)))
-  (let [(err (system (string-append "env GEMMA_COMMAND=gemma /gemma-wrapper/bin/gemma-wrapper --population \"" population "\" --name \"" name "\" --trait \"" trait-name "\" --verbose --loco --json --debug --parallel --input K.json -- -g BXD.8_geno.txt.gz -p pheno.txt -a BXD.8_snps.txt -lmm 2 -maf 0.1 > GWA.json")))]
-    (if (not (= err 0))
-        (exit err))))
+    ;; ---- to start GEMMA precompute inside container
+    ;; env TMPDIR=. LD_LIBRARY_PATH=$GUIX_ENVIRONMENT/lib/ guile -L . -s ./scripts/precompute/precompute-hits.scm
+    ;; --- First we compute K - control output goes to K.json
+    (let [(err (system (string-append "env GEMMA_COMMAND=gemma /gemma-wrapper/bin/gemma-wrapper --population \"" population "\" --name \"" name "\" --trait \"" trait-name "\" --verbose --loco --json --debug --parallel -- -gk -g BXD.8_geno.txt.gz -p " pheno-fn " -a BXD.8_snps.txt > K.json"  )))]
+      (if (not (= err 0))
+          (exit err)))
+    (let [(err (system (string-append "env GEMMA_COMMAND=gemma /gemma-wrapper/bin/gemma-wrapper --population \"" population "\" --name \"" name "\" --trait \"" trait-name "\" --verbose --loco --json --debug --parallel --input K.json -- -g BXD.8_geno.txt.gz -p " pheno-fn " -a BXD.8_snps.txt -lmm 2 -maf 0.1 > GWA.json")))]
+      (if (not (= err 0))
+          (exit err)))
+    (delete-file pheno-fn)
+    )
+  )
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