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-rw-r--r--gn/runner/gemma.scm43
-rwxr-xr-xscripts/precompute/precompute-hits.scm6
-rwxr-xr-xscripts/precompute/run-gemma.scm21
3 files changed, 42 insertions, 28 deletions
diff --git a/gn/runner/gemma.scm b/gn/runner/gemma.scm
index 131284a..4c1c374 100644
--- a/gn/runner/gemma.scm
+++ b/gn/runner/gemma.scm
@@ -10,16 +10,37 @@
#:use-module (rnrs base)
#:export (
+ write-pheno-file
run-gemma
))
+(define (write-pheno-file fn traits)
+ (define bxd-inds (geno-inds-bxd "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"))]
+ (format #t "~s ~s" ind outvalue)
+ (newline)
+ (display outvalue port)
+ (newline port))))
+ bxd-inds)
+ (close port)
+ ))
+)
+
(define (run-gemma population data-id probeset-id probesetfreeze-id name trait-name traits)
"Run gemma-wrapper to compute GRM and GWA. On failure the run will stop(!)"
- (define bxd-inds (geno-inds-bxd "BXD.json"))
(define ids (string-append (int-to-string data-id) ","
(int-to-string probeset-id) ","
(int-to-string probesetfreeze-id)))
- (assert (= 235 (length bxd-inds)))
(if name
(display (string-append "WE HAVE OUR " population " DATASET " name " and trait " trait-name " for precompute!\n")))
(display ids)
@@ -31,24 +52,6 @@
(pheno-fn (string-append tmpdir "/pheno.txt"))
(k-json-fn (string-append tmpdir "/K.json"))
(gwa-json-fn (string-append tmpdir "/GWA.json"))]
- (call-with-output-file pheno-fn
- (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)
- (close port)
- ))
-
- ;; 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
diff --git a/scripts/precompute/precompute-hits.scm b/scripts/precompute/precompute-hits.scm
index a18b33d..203dfbb 100755
--- a/scripts/precompute/precompute-hits.scm
+++ b/scripts/precompute/precompute-hits.scm
@@ -1,8 +1,8 @@
#! Precompute hits
-This is the obsolete script to compute GEMMA directly from the DB. We have split out
-this step into fetching traits and running gemma without DB. This allows scaling up
-on HPC etc.
+This is the *obsolete* script to compute GEMMA directly from the DB. We have split out
+this step into separate steps for (1) fetching traits and (2) running gemma without DB.
+This allows scaling up on HPC etc.
Run from base dir with
diff --git a/scripts/precompute/run-gemma.scm b/scripts/precompute/run-gemma.scm
index b14927a..36edf8b 100755
--- a/scripts/precompute/run-gemma.scm
+++ b/scripts/precompute/run-gemma.scm
@@ -5,9 +5,9 @@ GEMMA on those.
Run from base dir with
-guix shell guile guile-dbi -- guile -L ../.. -s run-gemma.scm --help
+ ~/opt/guix-pull/bin/guix shell guile guile-dbi guile-json -- guile -L . -e main -s scripts/precompute/run-gemma.scm 115476.json
-and with some extra paths
+and with some extra paths (for gemma)
. .guix-shell ruby --expose=/home/wrk/iwrk/opensource/code/genetics/gemma-wrapper/=/gemma-wrapper --expose=/home/wrk/iwrk/opensource/code/genetics/gemma/=/gemma -- env TMPDIR=tmp guile -L . -s ./scripts/precompute/run-gemma.scm
@@ -33,10 +33,21 @@ and with some extra paths
(help (single-char #\h) (value #f))))
(options (getopt-long args option-spec))
(help-wanted (option-ref options 'help #f))]
+ (display "RUNNING")
(if help-wanted
(format #t "list-traits-to-compute writes JSON traits files from the GN DB
Usage: list-traits-to-compute [options...]
-h, --help Display this help
-")
- (display "gemma-run")
-)))
+"))
+ (let [(trait-name "115475")]
+ (call-with-input-file "115475.json"
+ (lambda (port)
+ (let* [(json (json->scm port))
+ (dataset (assoc-ref json "traits"))
+ (dataset-name (car (car dataset)))
+ (traits (assoc-ref dataset dataset-name))
+ ]
+ (display dataset)
+ (write-pheno-file "pheno.txt" traits)
+ ; (run-gemma "BXD" data-id probeset-id probesetfreeze-id name trait-name traits)))
+ ))))))