diff options
Diffstat (limited to 'scripts/precompute')
| -rwxr-xr-x | scripts/precompute/list-traits-to-compute.scm | 2 | ||||
| -rwxr-xr-x | scripts/precompute/run-gemma.scm | 8 |
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 |