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#!/usr/bin/env guile \
-e main -s
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 . -e main -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;"
you can ignore the IPv6 message:
bind [::1]:3306: Cannot assign requested address
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 . -e main -s ./scripts/precompute/list-traits-to-compute.scm --next 1000
The current logic is to list all datasets that contain a
BXD. (bxd-strain-id-names #:used-for-mapping? #t) fetches all ids and
strain names listed in GN. Note that this differs from the actual
genotype file.
To find the StrainId in a dataset:
MariaDB [db_webqtl]> SELECT StrainId,value from ProbeSetData WHERE Id=115467;
+----------+---------+
| StrainId | value |
+----------+---------+
| 1 | 9.47169 |
| 2 | 9.21621 |
| 3 | 9.728 |
| 4 | 9.28976 |
| 5 | 9.55523 |
| 6 | 9.63562 ...
to speed things up a little we batch them up and check whether the BXD is part of it.
When that is the case we might as well write the phenotype file because we have the trait values.
!#
(use-modules (dbi dbi)
(gn db mysql)
(gn data dataset)
(gn data hits)
(gn data strains)
(gn util convert)
(gn runner gemma)
; (rnrs base)
(hashing sha-2)
(ice-9 getopt-long)
(ice-9 match)
(ice-9 textual-ports)
(json)
(rnrs bytevectors)
(srfi srfi-1)
(srfi srfi-9)
(srfi srfi-19) ; time
)
(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)
)
#!
The following is produced by gemma-wrapper as metadata
"meta": {
"type": "gemma-wrapper",
"version": "0.99.7-pre1",
"population": "BXD",
"name": "HC_U_0304_R",
"trait": "101500_at",
"url": "https://genenetwork.org/show_trait?trait_id=101500_at&dataset=HC_U_0304_R",
"archive_GRM": "46bfba373fe8c19e68be6156cad3750120280e2e-gemma-cXX.tar.xz",
"archive_GWA": "779a54a59e4cd03608178db4068791db4ca44ab3-gemma-GWA.tar.xz",
"dataid": 75629,
"probesetid": 1097,
"probesetfreezeid": 7
}
!#
(define (write-json-ld id name trait trait-name probesetfreeze-id probeset-id recs)
;; see also https://www.w3.org/2018/jsonld-cg-reports/json-ld/
(display id)
(display ":")
(display name)
(display ":")
(display trait-name)
(newline)
(let* [(traits (map (lambda (r)
(match r
[(strain-id . value) (cons (bxd-name strain-id) value)]
))
(reverse recs)))
(uri (format #f "https://genenetwork.org/show_trait?trait_id=~a&dataset=~a" trait-name name))
(sha256 (sha-256->string (sha-256 (string->utf8 (scm->json-string traits)))))
(json-data `(("@context" . "https://genenetwork.org/resource")
(type . traits)
(meta . ((version . "0.1")
(steps . ())
(sha256 . ((input-traits . ,sha256)))
(time . ,(date->string (time-utc->date (current-time))))))
(data .
((,id .
((group . "BXD")
(probesetfreeze-id . ,probesetfreeze-id)
(probeset-id . ,probeset-id)
(name . ,name)
(trait-name . ,trait-name)
(uri . ,uri)
(traits . ,traits)
))))))]
(call-with-output-file (string-append (number->string id) ".json")
(lambda (port)
(put-string port (scm->json-string json-data))))
))
(define (write-phenotypes first-id num batch-size)
(call-with-db
(lambda (db)
(begin
;; (let [(bxd-strains (memo-bxd-strain-id-names #:used-for-mapping? #t))]
(display "writing-phenotypes...")
(define (run-list-traits-to-compute db num prev-id)
;; ---- Build a query to collect num traits
(let* [(count (if (< batch-size num)
batch-size
num))
(rest (- num count))
(hits (get-precompute-hits db prev-id count))
(data-ids (map (lambda (h)
(hit-data-id h))
hits))
(data-str-ids (map (lambda (id) (string-append "Id=" (int-to-string id))) data-ids))
(data-ids-query (string-join data-str-ids " OR "))
(query (string-append "SELECT Id,StrainId,value FROM ProbeSetData WHERE " data-ids-query))
]
(display query)
(dbi-query db query)
;; ---- Walk each resulting trait and build a hash of data-id and list of trait values
(let [(id-traits (get-rows db '()))
(nrecs '())]
(for-each (lambda (r)
(let* [(data-id (assoc-ref r "Id"))
(strain-id (assoc-ref r "StrainId"))
(value (assoc-ref r "value"))
(has-lst (assoc-ref nrecs data-id))
(lst (if has-lst
(acons strain-id value has-lst)
`((,strain-id . ,value)))
)]
(set! nrecs (assoc-set! nrecs data-id lst))))
id-traits)
;; --- create the json output as a file by walking traits and hits
(for-each (lambda (h)
(let* [
(id (hit-data-id h))
(probeset-id (hit-probeset-id h))
(probesetfreeze-id (hit-probesetfreeze-id h))
(name (dataset-name db probesetfreeze-id))
(trait (get-trait db probeset-id))
(trait-name (assoc-ref trait "Name"))
(recs (assoc-ref nrecs id))
]
(if (has-bxd? recs)
(write-json-ld id name trait trait-name probesetfreeze-id probeset-id recs)
))) hits)
(if (> rest 0)
(run-list-traits-to-compute db rest (first (reverse data-ids)))) ;; start precompute
)))
(run-list-traits-to-compute db num first-id) ;; start precompute
))))
(define (main args)
;; (write args)
(let* ((option-spec '( (version (single-char #\v) (value #f))
(start-id (single-char #\s) (value #t))
(next (single-char #\n) (value #t))
(help (single-char #\h) (value #f))))
(options (getopt-long args option-spec))
(start-id (string->number (option-ref options 'start-id "0")))
(next (string->number (option-ref options 'next "5")))
(help-wanted (option-ref options 'help #f)))
(if help-wanted
(format #t "list-traits-to-compute writes JSON traits files from the GN DB
Usage: list-traits-to-compute [options...]
-s, --start-id num Start from ID (default 0)
-n, --next count In batches of count size (default 5)
-h, --help Display this help
")
(write-phenotypes start-id next 500) ;; batch size 500 appears to work best on my machine
)))
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