diff options
| -rw-r--r-- | test/lmm-integration-tests.scm | 16 |
1 files changed, 13 insertions, 3 deletions
diff --git a/test/lmm-integration-tests.scm b/test/lmm-integration-tests.scm index 7b9ca3e..90858ce 100644 --- a/test/lmm-integration-tests.scm +++ b/test/lmm-integration-tests.scm @@ -8,21 +8,31 @@ exec guile --debug -s "$0" "$@" #:use-module (srfi srfi-1) ; for last #:use-module (srfi srfi-13) #:use-module (srfi srfi-64) ; for tests + #:use-modules (ice-9 ftw) ; delete file #:use-module (ice-9 rdelim) ) +(define kinship-fn "./output/mouse_hs1940.cXX.txt") +(define gwa-fn "./output/mouse_hs1940.assoc.txt") + (test-begin "uvlmm-kinship-run") -(let [(err (system "./build/bin/Debug/gemma -g ./example/mouse_hs1940.geno.txt.gz -p ./example/mouse_hs1940.pheno.txt -gk -o mouse_hs1940 -debug"))] +(when (file-exists? kinship-fn) + (delete-file kinship-fn)) +(let [(err (system "./build/bin/Debug/gemma -g ./example/mouse_hs1940.geno.txt.gz -gk -o mouse_hs1940 -debug"))] (test-eqv 0 err)) (test-end "uvlmm-kinship-run") (test-begin "uvlmm-gwa-run") -(let [(err (system "./build/bin/Debug/gemma -g ./example/mouse_hs1940.geno.txt.gz -p ./example/mouse_hs1940.pheno.txt -n 1 -a ./example/mouse_hs1940.anno.txt -k ./output/mouse_hs1940.cXX.txt -o mouse_hs1940 -lmm 9 -debug"))] +(when (file-exists? gwa-fn) + (delete-file gwa-fn)) +;; The following integration test runs gemma uvlmm and adds up the output column as a check. +;; It uses the kinship-run matrix from the earlier test +(let [(err (system (string-append "./build/bin/Debug/gemma -g ./example/mouse_hs1940.geno.txt.gz -p ./example/mouse_hs1940.pheno.txt -n 1 -a ./example/mouse_hs1940.anno.txt -k " kinship-fn " -o mouse_hs1940 -lmm 9 -debug")))] (test-eqv 0 err)) -(call-with-input-file "output/mouse_hs1940.assoc.txt" +(call-with-input-file gwa-fn (lambda (port) (read-line port) ; skip first line (let* ((fields (string-split (read-line port) #\tab)) |