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#! Run from base dir with
.guix-shell -- guile -L . -s ./scripts/precompute/precompute-hits.scm
!#
(use-modules (dbi dbi)
(gn db mysql)
(gn data dataset)
(gn data hits)
(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)
(begin
;(newline)
; (dbi-query db "SELECT StrainId,Strain.Name FROM Strain, StrainXRef WHERE StrainXRef.StrainId = Strain.Id AND StrainXRef.InbredSetId = 1 AND Used_for_mapping='Y' ORDER BY StrainId;")
; (let [(row (get-row db))]
; (display row)
; )
;(let [(result (get-rows-apply db (lambda (r) `(,(assoc-ref r "StrainId") . ,(assoc-ref r "Name"))) '()))]
; (display (car result)))
;(newline)
(define bxd-strains (bxd-strain-id-names #:map? #t))
;(display (assoc 64728 bxd-strains))
;(newline)
;(newline)
;(dbi-query db "SELECT * FROM ProbeSetXRef LIMIT 3")
;(let [(row (get-row db))]
; (display row)
; )
;(db-check2 db)
;(newline)
;; ---- get first available dataset for precompute:
;; @@ order by dataid - recurse
(define (get-trait-name db probeset-id)
(dbi-query db (string-append "select Name,Symbol from ProbeSet where Id=" (int-to-string probeset-id) " limit 1"))
(get-row db)
)
(define (run-precompute db prev-id)
(let* [(hit (get-next-hit-for-precompute 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-name db probeset-id))
(trait-name (assoc-ref trait "Name"))
]
(display hit)
(display data-id)
(newline)
(define name (dataset-name db probesetfreeze-id))
;; ---- Get strains and phenotypes for this dataset
(dbi-query db (string-append "SELECT StrainId,value from ProbeSetData WHERE Id=" data-id-str))
(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
(if name
(display (string-append "WE HAVE OUR BXD DATASET " name " and trait " trait-name " for precompute!\n")))
(display data-id)
(display traits)
(newline)
))
(run-precompute db data-id)
))
(run-precompute db 0)
)))
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