diff options
Diffstat (limited to 'scripts')
| -rwxr-xr-x | scripts/precompute/precompute-hits.scm | 62 |
1 files changed, 35 insertions, 27 deletions
diff --git a/scripts/precompute/precompute-hits.scm b/scripts/precompute/precompute-hits.scm index 28dabc9..0088431 100755 --- a/scripts/precompute/precompute-hits.scm +++ b/scripts/precompute/precompute-hits.scm @@ -6,6 +6,7 @@ (use-modules (dbi dbi) (gn db mysql) + (gn data hits) (gn data strains) (gn util convert) (rnrs base) @@ -34,8 +35,8 @@ ;(newline) (define bxd-strains (bxd-strain-id-names #:map? #t)) - (display (assoc 64728 bxd-strains)) - (newline) + ;(display (assoc 64728 bxd-strains)) + ;(newline) ;(newline) ;(dbi-query db "SELECT * FROM ProbeSetXRef LIMIT 3") ;(let [(row (get-row db))] @@ -44,31 +45,38 @@ ;(db-check2 db) ;(newline) ;; ---- get first available dataset for precompute: - (dbi-query db "select Locus, DataId, ProbeSetId from ProbeSetXRef where Locus_old is NULL LIMIT 1") - (define hit (get-row db)) - (display hit) - (define data-id (assoc-ref hit "DataId")) - (display data-id) - (newline) - ;; ---- Get strains and phenotypes for this dataset - (dbi-query db (string-append "SELECT StrainId,value from ProbeSetData WHERE Id=" (int-to-string data-id))) - (define 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)]) - (if (assoc id bxd-strains) - lst - (append lst `(,id))))) + ;; @@ order by dataid - recurse + + + (define (run-precompute db prev-id) + (let* [(hit (get-next-hit-for-precompute db prev-id)) + (data-id (assoc-ref hit "DataId"))] + (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=" (int-to-string data-id))) + (define 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)]) + (if (assoc id bxd-strains) + lst + (append lst `(,id))))) - '() - traits)) - (if (= 0 (length non-bxd)) - (begin - (display "WE HAVE OUR BXD DATASET for precompute!") - (display traits) - (newline) + '() + traits)) + (if (= 0 (length non-bxd)) + (begin + (display "WE HAVE OUR BXD DATASET for precompute!\n") + (display data-id) + (display traits) + (newline) + )) + (run-precompute db data-id) )) + (run-precompute db 0) ))) |