precompute: pass in trait id for gemma

2 files changed, 6 insertions, 4 deletions

diff --git a/scripts/precompute/list-traits-to-compute.scm b/scripts/precompute/list-traits-to-compute.scm
index fbe89a6..9f900d1 100755
--- a/scripts/precompute/list-traits-to-compute.scm
+++ b/scripts/precompute/list-traits-to-compute.scm
@@ -149,7 +149,6 @@ The following is produced by gemma-wrapper as metadata
    (lambda (db)
    (begin
      ;; (let [(bxd-strains (memo-bxd-strain-id-names #:used-for-mapping? #t))]
-       (display "writing-phenotypes...")
        (define (run-list-traits-to-compute db num prev-id)
          ;; ---- Build a query to collect num traits
          (let* [(count (if (< batch-size num)
@@ -164,6 +163,7 @@ The following is produced by gemma-wrapper as metadata
                 (data-ids-query (string-join data-str-ids " OR "))
                 (query (string-append "SELECT Id,StrainId,value FROM ProbeSetData WHERE " data-ids-query))
                 ]
+           (format #t "writing-phenotypes from ~d to ~d batch ~d to ~d\n" first-id (+ first-id num) prev-id (+ prev-id count))
            (display query)
            (dbi-query db query)
            ;; ---- Walk each resulting trait and build a hash of data-id and list of trait values
diff --git a/scripts/precompute/run-gemma.scm b/scripts/precompute/run-gemma.scm
index 00cc68d..4952834 100755
--- a/scripts/precompute/run-gemma.scm
+++ b/scripts/precompute/run-gemma.scm
@@ -9,7 +9,7 @@ Run from base dir with
 
 and with some extra paths (for gemma)
 
-~/opt/guix-pull/bin/guix shell -C -F xz python python-lmdb tar time parallel coreutils-minimal guile guile-dbi guile-json ruby --expose=/home/wrk/iwrk/opensource/code/genetics/gemma-wrapper/=/gemma-wrapper --expose=/home/wrk/iwrk/opensource/code/genetics/gemma/=/gemma -- env TMPDIR=tmp GEMMA_COMMAND=/gemma/bin/gemma-0.98.5-linux-static-debug  guile -L . -e main -s ./scripts/precompute/run-gemma.scm test
+~/opt/guix-pull/bin/guix shell -C -F xz python python-lmdb tar time parallel coreutils-minimal guile guile-dbi guile-json ruby --expose=/home/wrk/iwrk/opensource/code/genetics/gemma-wrapper/=/gemma-wrapper --expose=/home/wrk/iwrk/opensource/code/genetics/gemma/=/gemma -- env TMPDIR=tmp GEMMA_COMMAND=/gemma/bin/gemma-0.98.5-linux-static-debug  guile -L . -e main -s ./scripts/precompute/run-gemma.scm --id 21529
 
 !#
 
@@ -30,6 +30,7 @@ and with some extra paths (for gemma)
   ;; (write args)
   (let* [
          (option-spec '( (version (single-char #\v) (value #f))
+                         (id      (value #t))
                          (help    (single-char #\h) (value #f))))
          (options (getopt-long args option-spec))
          (show-version (option-ref options 'version #f))
@@ -41,11 +42,12 @@ and with some extra paths (for gemma)
     (if help-wanted
         (format #t "run-gemma
 Usage: run-gemma [options...] filename(s)
+  --id               Run on identifier
   -v --version       Display version
   -h --help          Display this help
 ")
-        (let [(trait-id "115475")
-          (trait-fn "115475.json")
+        (let* [(trait-id (option-ref options 'id "0"))
+          (trait-fn (string-append trait-id ".json"))
           ]
 
       (call-with-input-file trait-fn