diff options
Diffstat (limited to 'gn')
| -rw-r--r-- | gn/data/hits.scm | 13 | ||||
| -rw-r--r-- | gn/runner/gemma.scm | 8 |
2 files changed, 18 insertions, 3 deletions
diff --git a/gn/data/hits.scm b/gn/data/hits.scm index 5108bd0..29d377b 100644 --- a/gn/data/hits.scm +++ b/gn/data/hits.scm @@ -15,6 +15,7 @@ #:export ( get-precompute-hit set-precompute-hit-status! + update-precompute! )) (define (get-precompute-hit db prev-id) @@ -22,9 +23,19 @@ (get-row db)) (define (set-precompute-hit-status! db data-id-str status-str) - "Set status of precompute record - typically 'RUN' or 'NON-BXD'. + "Set status of precompute record - typically from NULL to 'GEMMA-START' or 'NON-BXD'. +On completion it is set to 'GEMMA-DONE'. This is a temporary measure to get precompute going. Note we are counting on automated MariaDB transactions to not compete." (dbi-query db (string-append "UPDATE ProbeSetXRef SET Locus_old=\"" status-str "\" WHERE DataId=" data-id-str " AND Locus_old is NULL")) (ensure db) ) + +;; MariaDB [db_webqtl]> UPDATE ProbeSetXRef SET Locus_old=Locus,LRS_old=LRS,Locus="new",LRS=9.9,pValue=1.0,additive=1.0 WHERE ProbeSetFreezeId=1 AND DataId=2 AND Locus_old="GEMMA-START" ; + +(define (update-precompute! db data-id-str status-str locus lrs pvalue, additive) + "Once precompute is run we can update the table moving old values and plugging in the new. +" + (dbi-query db (string-append "UPDATE ProbeSetXRef SET Locus_old=Locus,LRS_old=LRS,Locus=\"" locus "\",LRS=" lrs ",pValue=" pvalue ",additive=" additive " WHERE DataId=" data-id-str " AND Locus_old is \"GEMMA-START\"")) + (ensure db) + ) diff --git a/gn/runner/gemma.scm b/gn/runner/gemma.scm index 2edb7b2..a31846a 100644 --- a/gn/runner/gemma.scm +++ b/gn/runner/gemma.scm @@ -13,10 +13,11 @@ )) (define (run-gemma population data-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")) (assert (= 235 (length bxd-inds))) (if name - (display (string-append "WE HAVE OUR BXD DATASET " name " and trait " trait-name " for precompute!\n"))) + (display (string-append "WE HAVE OUR " population " DATASET " name " and trait " trait-name " for precompute!\n"))) (display data-id) (display traits) (newline) @@ -38,7 +39,9 @@ (newline) (display outvalue port) (newline port)))) - bxd-inds))) + bxd-inds) + (close port) + )) ;; set up with ./.guix-shell -- guile -L . -s ./scripts/precompute/precompute-hits.scm @@ -56,4 +59,5 @@ (delete-file k-json-fn) (rmdir tmpdir) ) + #t ) |