diff options
| -rw-r--r-- | gn/data/strains.scm | 5 | ||||
| -rw-r--r-- | gn/db/mysql.scm | 2 | ||||
| -rw-r--r-- | gn/util/convert.scm | 14 | ||||
| -rwxr-xr-x | scripts/precompute/precompute-hits.scm | 35 |
4 files changed, 50 insertions, 6 deletions
diff --git a/gn/data/strains.scm b/gn/data/strains.scm index 241ecda..39fe71e 100644 --- a/gn/data/strains.scm +++ b/gn/data/strains.scm @@ -7,8 +7,9 @@ #:use-module (ice-9 string-fun) ;; #:use-module (gn db sparql) #:use-module (dbi dbi) - #:use-module (gn db mysql) #:use-module (gn data group) + #:use-module (gn db mysql) + #:use-module (gn util convert) #:use-module (web gn-uri) #:export ( @@ -24,7 +25,7 @@ map? will say whether the strains/individuals are used for mapping. " (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 = " (format #f "~d" inbred-set) + (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 map? " AND Used_for_mapping='Y'" "") diff --git a/gn/db/mysql.scm b/gn/db/mysql.scm index 4e2b280..fb7093a 100644 --- a/gn/db/mysql.scm +++ b/gn/db/mysql.scm @@ -50,7 +50,7 @@ (dbi-get_row db)) (define (get-rows db list) - "After running dbi-query we can fetch all rows and return them as a list of records, which are assoc list: + "After running dbi-query we can fetch all rows and return them as a list of records, which is an alist: (dbi-query db \"SELECT StrainId,Strain.Name FROM Strain, StrainXRef WHERE StrainXRef.StrainId = Strain.Id AND StrainXRef.InbredSetId = 1 ORDER BY StrainId;\") (db-check db) diff --git a/gn/util/convert.scm b/gn/util/convert.scm new file mode 100644 index 0000000..ff943e0 --- /dev/null +++ b/gn/util/convert.scm @@ -0,0 +1,14 @@ +(define-module (gn util convert) + #: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) + + #:export ( + int-to-string + )) + +(define (int-to-string i) + (format #f "~d" i)) 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) + )) ))) |