From ad07fc167c4f35490fd59e687aac1f4291defcc2 Mon Sep 17 00:00:00 2001
From: Lei Yan
Date: Tue, 4 Feb 2014 11:35:41 -0600
Subject: On branch master

---
 wqflask/maintenance/dataset/genotypes.py | 13 +++++++++++++
 wqflask/maintenance/dataset/probesets.py | 18 +++++++++++++++---
 2 files changed, 28 insertions(+), 3 deletions(-)
 create mode 100644 wqflask/maintenance/dataset/genotypes.py

(limited to 'wqflask')

diff --git a/wqflask/maintenance/dataset/genotypes.py b/wqflask/maintenance/dataset/genotypes.py
new file mode 100644
index 00000000..c83fb8b7
--- /dev/null
+++ b/wqflask/maintenance/dataset/genotypes.py
@@ -0,0 +1,13 @@
+import utilities
+
+def get_geno(inbredsetid, name):
+    cursor = utilities.get_cursor()
+    sql = """
+        SELECT Geno.`Id`, Geno.`Name`, Geno.`Chr`, Geno.`Mb`
+        FROM (Geno, InbredSet)
+        WHERE Geno.`SpeciesId`=InbredSet.`SpeciesId`
+        AND InbredSet.`Id`=%s
+        AND Geno.`Name` LIKE %s
+        """
+    cursor.execute(sql, (inbredsetid, name))
+    return cursor.fetchone()
diff --git a/wqflask/maintenance/dataset/probesets.py b/wqflask/maintenance/dataset/probesets.py
index 2c755203..06b9a394 100644
--- a/wqflask/maintenance/dataset/probesets.py
+++ b/wqflask/maintenance/dataset/probesets.py
@@ -1,6 +1,7 @@
 import sys
 
 import utilities
+import genotypes
 
 def get_probesetxref(probesetfreezeid):
     cursor = utilities.get_cursor()
@@ -47,7 +48,7 @@ def get_probesetxref_probesetfreezeid(locus, probesetfreezeid):
 def get_probesetxref_inbredsetid(locus, inbredsetid):
     cursor = utilities.get_cursor()
     sql = """
-        SELECT ProbeSetXRef.`ProbeSetId`
+        SELECT ProbeSetXRef.`ProbeSetId`, ProbeSetXRef.`mean`, ProbeSetXRef.`LRS`, ProbeSetXRef.`Locus`
         FROM (ProbeSetXRef, ProbeSetFreeze, ProbeFreeze)
         WHERE ProbeSetXRef.`ProbeSetFreezeId`=ProbeSetFreeze.`Id`
         AND ProbeSetFreeze.`ProbeFreezeId`=ProbeFreeze.`Id`
@@ -64,8 +65,19 @@ def get_normalized_probeset(locus, inbredsetid):
         normalized_probeset = []
         probesetid = probesetxref[0]
         probeset = get_probeset(probesetid)
-        normalized_probeset.append(probeset)
+        normalized_probeset.append(probeset[1])
+        normalized_probeset.append(probeset[2])
+        normalized_probeset.append(probeset[3])
+        normalized_probeset.append(probeset[4])
+        normalized_probeset.append(probeset[5])
+        normalized_probeset.append(probeset[6])
+        normalized_probeset.append(probesetxref[1])
+        normalized_probeset.append(probesetxref[2])
+        locus = probesetxref[3]
+        geno = genotypes.get_geno(inbredsetid=inbredsetid, name=locus)
+        normalized_probeset.append(geno[2])
+        normalized_probeset.append(geno[3])
         normalized_probesets.append(normalized_probeset)
-    print normalized_probesets
+    print normalized_probesets[:2]
 
 get_normalized_probeset(locus="rs3663871", inbredsetid=1)
-- 
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