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(define-module (gn data strains)
#:use-module (json)
#:use-module (ice-9 match)
#:use-module (ice-9 format)
#:use-module (ice-9 iconv)
#:use-module (ice-9 receive)
#:use-module (ice-9 string-fun)
;; #:use-module (gn db sparql)
#:use-module (dbi dbi)
#:use-module (gn data group)
#:use-module (gn db mysql)
#:use-module (gn util convert)
#:use-module (web gn-uri)
#:export (
strain-id-names
bxd-strain-id-names
))
(define* (strain-id-names inbred-set #:key (used-for-mapping? #t))
"Return assoc list of tuples of strain id+names:
((4 . BXD1) (5 . BXD2) (6 . BXD5) (7 . BXD6)...
used-for-mapping? will say whether the strains/individuals are used for mapping. Always True, FIXME
"
(call-with-db
(lambda (db)
(dbi-query db (string-append "SELECT StrainId,Strain.Name FROM Strain, StrainXRef WHERE StrainXRef.StrainId = Strain.Id AND StrainXRef.InbredSetId = " (int-to-string inbred-set)
(if used-for-mapping?
;; " AND Used_for_mapping='Y'"
"")
" ORDER BY StrainId;"))
(get-rows-apply db (lambda (r) `(,(assoc-ref r "StrainId") . ,(assoc-ref r "Name"))) '()))))
(define* (bxd-strain-id-names #:key (used-for-mapping? #f))
"Return assoc list of tuples of strain id + names. Same as strain-id-names, but just for the BXD
used-for-mapping? will say whether the strains/individuals are used for mapping. Always True, FIXME"
(filter (lambda (l) l)
(map (lambda (l)
(let [(id (car l))
(name (cdr l))]
(if (or (< id 42) (string-contains name "BXD"))
l
#f))
) (strain-id-names 1 #:used-for-mapping? used-for-mapping?))))
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