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-rwxr-xr-xscripts/precompute/run-gemma.scm21
1 files changed, 13 insertions, 8 deletions
diff --git a/scripts/precompute/run-gemma.scm b/scripts/precompute/run-gemma.scm
index e6a4e26..9a7bba2 100755
--- a/scripts/precompute/run-gemma.scm
+++ b/scripts/precompute/run-gemma.scm
@@ -39,15 +39,20 @@ and with some extra paths (for gemma)
Usage: list-traits-to-compute [options...]
-h, --help Display this help
"))
- (let [(trait-name "115475")]
- (call-with-input-file "115475.json"
+ (let [(trait-id "115475")
+ (trait-fn "115475.json")
+ ]
+
+ (call-with-input-file trait-fn
(lambda (port)
(let* [(json (json->scm port))
- (dataset (assoc-ref json "traits"))
- (dataset-name (car (car dataset)))
- (traits (assoc-ref dataset dataset-name))
+ (dataset (car (assoc-ref json "data")))
+ (data (cdr dataset))
+ (dataset-name (assoc-ref data "name"))
+ (trait-name (assoc-ref data "trait-name"))
+ (traits (assoc-ref data "traits"))
+ (pheno-fn (string-append trait-id "-pheno.txt"))
]
- (display dataset)
- (write-pheno-file "pheno.txt" traits)
- (invoke-gemma-wrapper-loco dataset-name trait-name "pheno.txt")
+ (write-pheno-file pheno-fn traits)
+ (invoke-gemma-wrapper-loco dataset-name trait-name trait-fn pheno-fn)
))))))