diff options
| author | Pjotr Prins | 2023-11-18 12:33:22 +0100 |
|---|---|---|
| committer | Pjotr Prins | 2023-11-18 12:33:22 +0100 |
| commit | b1db013cc01c94e27edf982be9b027a2b0bb9712 (patch) | |
| tree | 9aa73c1c8bbff2f7659f229c08b395788c6f33ec /gn | |
| parent | 06f941636a99904671c89916e17f28de4b2cd07e (diff) | |
| download | gn-guile-b1db013cc01c94e27edf982be9b027a2b0bb9712.tar.gz | |
Get first BXD dataset for precompute
Diffstat (limited to 'gn')
| -rw-r--r-- | gn/data/strains.scm | 5 | ||||
| -rw-r--r-- | gn/db/mysql.scm | 2 | ||||
| -rw-r--r-- | gn/util/convert.scm | 14 |
3 files changed, 18 insertions, 3 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)) |