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#!
Step p1 lists traits that need to be computed.
This is a script that fetches trait IDs from the GN database
directly. The direct database calls are used right now and ought to be
turned into a REST API.
Run from base dir with
. .guix-shell -- guile -L . -s ./scripts/precompute/list-traits-to-compute.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
test connection with mysql client:
mysql -uwebqtlout -pwebqtlout -A -h 127.0.0.1 -P 3306 db_webqtl -e "show tables;"
to create a clean slate, for now, update Locus_old with
update ProbeSetXRef set Locus_old=NULL;
you should see
MariaDB [db_webqtl]> select count(Locus_old) from ProbeSetXRef where Locus_old != NULL limit 5;
+------------------+
| count(Locus_old) |
+------------------+
| 0 |
+------------------+
Now list the next 1000 trait IDs:
. .guix-shell -- guile -L . -s ./scripts/precompute/list-traits-to-compute.scm --next 1000
!#
(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)
)
(call-with-db
(lambda (db)
(begin
(define bxd-strains (bxd-strain-id-names #:used-for-mapping? #t))
(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-list-traits-to-compute db prev-id count)
(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)
(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))
(if (eq? non-bxd '())
(set-precompute-hit-status! db data-id-str "GEMMA-START")
;; disable precompute if non-bxd, for now, so it won't try again
(set-precompute-hit-status! db data-id-str "NON-BXD"))
(if (> count 0)
(run-list-traits-to-compute db data-id (- count 1)) ;; next round
)
))))
(run-list-traits-to-compute db 0 5) ;; start precompute
)))
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