diff options
Diffstat (limited to 'scripts/precompute/precompute-hits.scm')
| -rwxr-xr-x | scripts/precompute/precompute-hits.scm | 90 |
1 files changed, 46 insertions, 44 deletions
diff --git a/scripts/precompute/precompute-hits.scm b/scripts/precompute/precompute-hits.scm index 0fabe8f..7385995 100755 --- a/scripts/precompute/precompute-hits.scm +++ b/scripts/precompute/precompute-hits.scm @@ -64,49 +64,51 @@ ssh -L 3306:127.0.0.1:3306 -f -N tux02.genenetwork.org ) (define (run-precompute db prev-id) - (let* [(hit (get-precompute-hit db prev-id)) - (data-id (assoc-ref hit "DataId")) - (data-id-str (int-to-string data-id)) - (probesetfreeze-id (assoc-ref hit "ProbeSetFreezeId")) - (probeset-id (assoc-ref hit "ProbeSetId")) - (trait (get-trait db probeset-id)) - (trait-name (assoc-ref trait "Name")) - (name (dataset-name db probesetfreeze-id)) - ] - (display hit) - (display data-id) - (newline) - ;; ---- Get strains and phenotypes for this dataset - (dbi-query db (string-append "SELECT StrainId,value from ProbeSetData WHERE Id=" data-id-str)) - (define id_traits (get-rows-apply db - (lambda (r) `(,(assoc-ref r "StrainId") . ,(assoc-ref r "value"))) - '())) - ;; ---- Now we need to make sure that all strains belong to BXD - (define non-bxd (fold - (lambda (strain lst) - (let* [(id (car strain)) - (name (assoc id bxd-strains))] - (if name - lst - (append lst `(,name))))) + (let [(hit (get-precompute-hit db prev-id))] + (if hit + (let* [(data-id (assoc-ref hit "DataId")) + (data-id-str (int-to-string data-id)) + (probesetfreeze-id (assoc-ref hit "ProbeSetFreezeId")) + (probeset-id (assoc-ref hit "ProbeSetId")) + (trait (get-trait db probeset-id)) + (trait-name (assoc-ref trait "Name")) + (name (dataset-name db probesetfreeze-id)) + ] + (display hit) + (display data-id) + (newline) + ;; ---- Get strains and phenotypes for this dataset + (dbi-query db (string-append "SELECT StrainId,value from ProbeSetData WHERE Id=" data-id-str)) + (define id_traits (get-rows-apply db + (lambda (r) `(,(assoc-ref r "StrainId") . ,(assoc-ref r "value"))) + '())) + ;; ---- Now we need to make sure that all strains belong to BXD + (define non-bxd (fold + (lambda (strain lst) + (let* [(id (car strain)) + (name (assoc id bxd-strains))] + (if name + lst + (append lst `(,name))))) - '() - id_traits)) - (define traits (map - (lambda (t) - (match t - ((id . value) (cons (assoc-ref bxd-strains id) value) - ))) - id_traits)) - (display traits) - ;; (if (= 0 (length non-bxd)) - (if (eq? non-bxd '()) - (begin - (set-precompute-hit-status! db data-id-str "GEMMA-START") - (run-gemma "BXD" data-id name trait-name traits))) - ;; disable precompute if non-bxd, for now, so it won't try again - (set-precompute-hit-status! db data-id-str "NON-BXD") - ;;(run-precompute db data-id) - )) - (run-precompute db 0) + '() + id_traits)) + (define traits (map + (lambda (t) + (match t + ((id . value) (cons (assoc-ref bxd-strains id) value) + ))) + id_traits)) + (display traits) + ;; (if (= 0 (length non-bxd)) + (if (eq? non-bxd '()) + (begin + (set-precompute-hit-status! db data-id-str "GEMMA-START") + (run-gemma "BXD" data-id name trait-name traits) + (set-precompute-hit-status! db data-id-str "GEMMA-DONE"))) + ;; disable precompute if non-bxd, for now, so it won't try again + (set-precompute-hit-status! db data-id-str "NON-BXD") + (run-precompute db data-id) ;; next round + )))) + (run-precompute db 0) ;; start precompute ))) |