4 files changed, 61 insertions, 12 deletions
diff --git a/gn/data/hits.scm b/gn/data/hits.scm
index f7ce49e..85c4912 100644
--- a/gn/data/hits.scm
+++ b/gn/data/hits.scm
@@ -5,6 +5,7 @@
   #:use-module (ice-9 iconv)
   #:use-module (ice-9 receive)
   #:use-module (ice-9 string-fun)
+  #:use-module (srfi srfi-9)
   ;; #:use-module (gn db sparql)
   #:use-module (dbi dbi)
   #:use-module (gn db mysql)
@@ -17,11 +18,26 @@
             get-precompute-hit
             set-precompute-hit-status!
             update-precompute!
+            hit-data-id
+            hit-probeset-id
+            hit-probesetfreeze-id
             ))
 
-(define (get-precompute-hits db prev-id num)
-  (dbi-query db (string-append "select Locus, DataId, ProbeSetId, ProbeSetFreezeId from ProbeSetXRef where DataId>" (int-to-string prev-id) " AND Locus_old is NULL ORDER BY DataId LIMIT " (format #f "~d" num)))
-  (get-rows db '()))
+
+(define-record-type <hit>
+  (make-hit data-id probeset-id probesetfreeze-id)
+  hit?
+  (data-id hit-data-id)
+  (probeset-id hit-probeset-id)
+  (probesetfreeze-id hit-probesetfreeze-id)
+  )
+
+(define (get-precompute-hits db first-id num)
+  (dbi-query db (string-append "select Locus, DataId, ProbeSetId, ProbeSetFreezeId from ProbeSetXRef where DataId>" (int-to-string first-id) " AND Locus_old is NULL ORDER BY DataId LIMIT " (int-to-string num)))
+  (map (lambda (r)
+         (make-hit (assoc-ref r "DataId") (assoc-ref r "ProbeSetId") (assoc-ref r "ProbeSetFreezeId")))
+         (get-rows db '())
+  ))
 
 (define (get-precompute-hit db prev-id)
   (car (get-precompute-hits db prev-id 1)))
diff --git a/gn/db/sources/wikidata.scm b/gn/db/sources/wikidata.scm
new file mode 100644
index 0000000..7397426
--- /dev/null
+++ b/gn/db/sources/wikidata.scm
@@ -0,0 +1,29 @@
+#!
+
+Wikidata queries
+
+!#
+
+(define-module (gn db sources wikidata)
+)
+
+(define ps-encoded-by "ps:P702")
+(define wdt-instance-of "wdt:P31")
+(define wdt-in-taxon "wdt:P703")
+(define wd-human "wd:Q15978631")
+(define wd-mouse "wd:Q83310")
+(define wd-rat "wd:Q184224")
+(define wd-gene "wd:Q7187")
+
+(define (wikidata_query_geneids gene_name)
+  "Return the wikidata identifiers pointing to genes of listed species"
+  (string-append
+     "SELECT DISTINCT ?wikidata_id
+            WHERE {
+              ?wikidata_id " wdt-instance-of " " wd-gene ";
+                           " wdt-in-taxon " ?species .
+              VALUES (?species) { (" wd-human " ) ( " wd-mouse" ) ( " wd-rat" ) } .
+              ?wikidata_id rdfs:label \"" gene_name "\"@en .
+        }
+"
+              ))
diff --git a/gn/db/sparql.scm b/gn/db/sparql.scm
index b7d94f3..f03389b 100644
--- a/gn/db/sparql.scm
+++ b/gn/db/sparql.scm
@@ -2,7 +2,7 @@
 
 Module for handling SPARQL primitives.
 
-Note that GN queries should go into gn/data - this is currently not
+Note that GN queries should go into gn/db/sources - this is currently not
 the case.
 
 !#
@@ -18,6 +18,7 @@ the case.
   #:use-module (web request)
   #:use-module (web uri)
   #:use-module (gn cache memoize)
+  #:use-module (gn db sources wikidata)
   #:use-module (web gn-uri)
 
   #:export (memo-sparql-species
diff --git a/gn/runner/gemma.scm b/gn/runner/gemma.scm
index 69991dd..9a5c0fc 100644
--- a/gn/runner/gemma.scm
+++ b/gn/runner/gemma.scm
@@ -39,24 +39,27 @@
       ))
 )
 
-(define (invoke-gemma-wrapper-loco name trait-name pheno-fn)
+(define (invoke-gemma-wrapper-loco name trait-name trait-fn pheno-fn geno-fn)
   "Create a tmpdir and invoke gemma-wrapper using parallel LOCO. Note that at this point we use a number of defaults for BXD"
   (let* [(population "BXD")
          (sys-tmpdir (getenv "TMPDIR"))
          (tmpdir (mkdtemp (string-append sys-tmpdir "/run-gemma-XXXXXX")))
          (k-json-fn (string-append tmpdir "/K.json"))
-         (gwa-json-fn (string-append tmpdir "/GWA.json"))]
+         (gwa-json-fn (string-append tmpdir "/GWA.json"))
+         (trait-json-fn (string-append tmpdir "/" trait-fn))]
+    (copy-file trait-fn trait-json-fn)
     ;; --- First we compute K - control output goes to K.json
-    (let [(err (system (string-append "/gemma-wrapper/bin/gemma-wrapper --verbose --population \"" population "\" --name \"" name "\" --trait \"" trait-name "\" --verbose --loco --json --parallel -- -gk -g BXD.8_geno.txt.gz -p " pheno-fn " -a BXD.8_snps.txt > " k-json-fn  )))]
+    (let [(err (system (string-append "/gemma-wrapper/bin/gemma-wrapper --verbose --population \"" population "\" --name \"" name "\" --trait \"" trait-name "\" --verbose --loco --json --parallel -- -gk -g " geno-fn " -p " pheno-fn " -a BXD.8_snps.txt > " k-json-fn  )))]
       (if (not (= err 0))
           (exit err)))
-    (let [(err (system (string-append "/gemma-wrapper/bin/gemma-wrapper --population \"" population "\" --name \"" name "\" --id \"" trait-name "\" --trait \"" trait-name "\" --verbose --loco --json --input " k-json-fn " -- -g BXD.8_geno.txt.gz -p " pheno-fn " -a BXD.8_snps.txt -lmm 9 -maf 0.1 > " gwa-json-fn)))]
+    (let [(err (system (string-append "/gemma-wrapper/bin/gemma-wrapper --meta \"" trait-json-fn "\" --population \"" population "\" --name \"" name "\" --id \"" trait-name "\" --trait \"" trait-name "\" --verbose --loco --json --lmdb --input " k-json-fn " -- -g " geno-fn " -p " pheno-fn " -a BXD.8_snps.txt -lmm 9 -maf 0.1 > " gwa-json-fn)))]
       (if (not (= err 0))
           (exit err)))
-    ;; (delete-file pheno-fn)
-    ;; (delete-file gwa-json-fn)
-    ;; (delete-file k-json-fn)
-    ;; (rmdir tmpdir)
+    (delete-file pheno-fn)
+    (delete-file gwa-json-fn)
+    (delete-file k-json-fn)
+    (delete-file trait-json-fn)
+    (rmdir tmpdir)
     )
   )