1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
|
(define-module (gn data dataset)
#: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 (srfi srfi-1)
#:use-module (dbi dbi)
#:use-module (gn db mysql)
#:use-module (gn data genotype)
#:use-module (gn data group)
#:use-module (gn util convert)
#:use-module (web gn-uri)
#:use-module (rnrs base) ; for assert
#:export (
dataset-name
get-bxd-publish-list
get-bxd-publish-values-list
get-bxd-publish-name-value-dict
get-bxd-publish-dataid-name-value-dict
))
(define (get-dataset db probesetfreeze-id)
(dbi-query db
(string-append
"select Name,Name2,FullName from ProbeSetFreeze where Id=" (int-to-string probesetfreeze-id) " limit 1;"))
(get-row db))
(define (dataset-name db probesetfreeze-id)
(assoc-ref (get-dataset db probesetfreeze-id) "Name"))
(define (get-dataid-from-publishxrefid id)
"Get the internal dataid from publishxref - which is the same as used in the GN2 web interface"
(call-with-db
(lambda (db)
(let [(query (string-append "SELECT Id,PhenotypeId,DataId FROM PublishXRef WHERE Id=" id " AND InbredSetId=1 LIMIT 1"))]
(dbi-query db query)
(pk (int-to-string (assoc-ref (get-row db) "DataId")))))))
(define (get-bxd-publish-list)
(call-with-db
(lambda (db)
(let [(query "SELECT Id,PhenotypeId,DataId FROM PublishXRef WHERE InbredSetId=1")]
(dbi-query db query)
(get-rows db '())))))
(define* (get-bxd-publish-values-list dataid #:optional used-for-mapping?)
"Returns dict of name values , e.g. [{\"Name\":\"C57BL/6J\",\"value\":9.136},{\"Name\":\"DBA/2J\",\"value\":4.401},{\"Name\":\"BXD9\",\"value\":4.36}, ... used-for-mapping? skips the founders and maybe other unmappable inds. Note, currently unused."
(call-with-db
(lambda (db)
(let [(query (string-append "SELECT Strain.Name, PublishData.value FROM Strain, PublishData WHERE PublishData.Id=" dataid " and Strain.Id=StrainID;"))]
(dbi-query db query)
(if used-for-mapping?
(remove null? (pk (get-rows-apply db
(lambda (r)
(if (string-contains (assoc-ref r "Name") "BXD")
`(("Name" . ,(assoc-ref r "Name")) ("value" . ,(assoc-ref r "value")))
'() ) ;; return empty on no match
) '())))
(get-rows db '())
)))))
(define* (get-bxd-publish-dataid-name-value-dict dataid #:optional used-for-mapping?)
"Returns dict of name values, e.g. (((\"C57BL/6J\" . 9.136) (\"DBA/2J\" . 4.401) (\"BXD9\" . 4.36) ... used-for-mapping? skips the founders and maybe other unmappable inds."
(call-with-db
(lambda (db)
(let [(query (string-append "SELECT Strain.Name, PublishData.value FROM Strain, PublishData WHERE PublishData.Id=" dataid " and Strain.Id=StrainID;"))]
(dbi-query db query)
(if used-for-mapping?
(remove null? (pk (get-rows-apply db
(lambda (r)
(if (string-contains (assoc-ref r "Name") "BXD")
`(,(assoc-ref r "Name") . ,(assoc-ref r "value"))
'() ) ;; return empty on no match
) '())))
(remove null? (pk (get-rows-apply db
(lambda (r)
`(,(assoc-ref r "Name") . ,(assoc-ref r "value"))
) '())))
)))))
(define* (get-bxd-publish-name-value-dict id #:optional used-for-mapping?)
"Same as above function, but starting from data id"
(get-bxd-publish-dataid-name-value-dict (get-dataid-from-publishxrefid id) used-for-mapping?))
|
