#! Run from base dir with . .guix-shell -- guile -L . -s ./scripts/precompute/precompute-hits.scm and with some extra paths . .guix-shell ruby --expose=/home/wrk/iwrk/opensource/code/genetics/gemma-wrapper/=/gemma-wrapper --expose=/home/wrk/iwrk/opensource/code/genetics/gemma/=/gemma -- env TMPDIR=tmp guile -L . -s ./scripts/precompute/precompute-hits.scm You may want to forward a mysql port if there is no DB locally ssh -L 3306:127.0.0.1:3306 -f -N tux02.genenetwork.org !# (use-modules (dbi dbi) (gn db mysql) (gn data dataset) (gn data hits) (gn data strains) (gn util convert) (gn runner gemma) ; (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))) ;; ---- fetch all known BXD sample/individual/strain names (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 db probeset-id) (dbi-query db (string-append "select Id,Chr,Mb,Name,Symbol,description from ProbeSet where Id=" (int-to-string probeset-id) " limit 1")) (get-row db) ) (define (run-precompute db prev-id) (let [(hit (get-precompute-hit db prev-id))] (if hit (let* [(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 db probeset-id)) (trait-name (assoc-ref trait "Name")) (name (dataset-name db probesetfreeze-id)) ] (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=" data-id-str)) (define id_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)) (name (assoc id bxd-strains))] (if name lst (append lst `(,name))))) '() id_traits)) (define traits (map (lambda (t) (match t ((id . value) (cons (assoc-ref bxd-strains id) value) ))) id_traits)) ;; (display traits) ;; (if (= 0 (length non-bxd)) (if (eq? non-bxd '()) (begin (set-precompute-hit-status! db data-id-str "GEMMA-START") (run-gemma "BXD" data-id probeset-id probesetfreeze-id name trait-name traits) (set-precompute-hit-status! db data-id-str "GEMMA-DONE")) ;; disable precompute if non-bxd, for now, so it won't try again (set-precompute-hit-status! db data-id-str "NON-BXD")) (run-precompute db data-id) ;; next round )))) (run-precompute db 0) ;; start precompute )))