diff options
Diffstat (limited to 'scripts/precompute/run-gemma.scm')
| -rwxr-xr-x | scripts/precompute/run-gemma.scm | 42 |
1 files changed, 27 insertions, 15 deletions
diff --git a/scripts/precompute/run-gemma.scm b/scripts/precompute/run-gemma.scm index e6a4e26..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 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 +~/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 !# @@ -30,24 +30,36 @@ 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)) (help-wanted (option-ref options 'help #f))] - (display "RUNNING") + (if show-version + (begin + (display "run-gemma version 1.0\n") + (exit))) (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 -")) - (let [(trait-name "115475")] - (call-with-input-file "115475.json" + (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 (option-ref options 'id "0")) + (trait-fn (string-append trait-id ".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 "BXD.8_geno.txt.gz") + ))))))) |