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-rwxr-xr-xscripts/precompute/precompute-hits.scm35
1 files changed, 32 insertions, 3 deletions
diff --git a/scripts/precompute/precompute-hits.scm b/scripts/precompute/precompute-hits.scm
index a6617d9..28dabc9 100755
--- a/scripts/precompute/precompute-hits.scm
+++ b/scripts/precompute/precompute-hits.scm
@@ -7,14 +7,19 @@
(use-modules (dbi dbi)
(gn db mysql)
(gn data strains)
+ (gn util convert)
(rnrs base)
(ice-9 match)
+ (srfi srfi-1)
)
;; potentially you want to test connection with mysql client:
;;
;; mysql -uwebqtlout -pwebqtlout -A -h 127.0.0.1 -P 3306 db_webqtl -e "show tables;"
;;
+;; for now update Locus_old with
+;;
+;; update ProbeSetXRef set Locus_old=NULL;
(call-with-db
(lambda (db)
@@ -38,8 +43,32 @@
; )
;(db-check2 db)
;(newline)
- ;; get first dataset for precompute
- (dbi-query db "select ProbeSetId, Locus, DataId from ProbeSetXRef where Locus_old is NULL LIMIT 1")
- (display (get-row db))
+ ;; ---- 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)))))
+
+ '()
+ traits))
+ (if (= 0 (length non-bxd))
+ (begin
+ (display "WE HAVE OUR BXD DATASET for precompute!")
+ (display traits)
+ (newline)
+ ))
)))