Merge /home/zas1024/gene

1 files changed, 0 insertions, 90 deletions

diff --git a/wqflask/maintenance/dataset/probesets.py b/wqflask/maintenance/dataset/probesets.py
deleted file mode 100644
index 97bb5bdf..00000000
--- a/wqflask/maintenance/dataset/probesets.py
+++ /dev/null
@@ -1,90 +0,0 @@
-import utilities
-import datastructure
-import genotypes
-
-def get_probesetxref(probesetfreezeid):
-    cursor = utilities.get_cursor()
-    sql = """
-        SELECT ProbeSetXRef.`ProbeSetId`, ProbeSetXRef.`DataId`
-        FROM ProbeSetXRef
-        WHERE ProbeSetXRef.`ProbeSetFreezeId`=%s
-        """
-    cursor.execute(sql, (probesetfreezeid))
-    return cursor.fetchall()
-    
-def get_probeset(probesetid):
-    cursor = utilities.get_cursor()
-    sql = """
-        SELECT ProbeSet.`Id`, ProbeSet.`Name`, ProbeSet.`Symbol`, ProbeSet.`description`, ProbeSet.`Probe_Target_Description`, ProbeSet.`Chr`, ProbeSet.`Mb`
-        FROM ProbeSet
-        WHERE ProbeSet.`Id`=%s
-        """
-    cursor.execute(sql, (probesetid))
-    return cursor.fetchone()
-    
-def get_probesetdata(probesetdataid):
-    cursor = utilities.get_cursor()
-    sql = """
-        SELECT Strain.`Id`, Strain.`Name`, ProbeSetData.`value`
-        FROM ProbeSetData, Strain
-        WHERE ProbeSetData.`Id`=%s
-        AND ProbeSetData.`StrainId`=Strain.`Id`;
-        """
-    cursor.execute(sql, (probesetdataid))
-    return cursor.fetchall()
-
-def get_probesetxref_probesetfreezeid(locus, probesetfreezeid):
-    cursor = utilities.get_cursor()
-    sql = """
-        SELECT ProbeSetXRef.`ProbeSetId`
-        FROM ProbeSetXRef
-        WHERE ProbeSetXRef.`ProbeSetFreezeId`=%s
-        AND ProbeSetXRef.`Locus` LIKE %s
-        """
-    cursor.execute(sql, (probesetfreezeid, locus))
-    return cursor.fetchall()
-    
-def get_probesetxref_inbredsetid(locus, inbredsetid):
-    cursor = utilities.get_cursor()
-    sql = """
-        SELECT ProbeSetXRef.`ProbeSetId`, ProbeSetXRef.`mean`, ProbeSetXRef.`LRS`, ProbeSetXRef.`Locus`, ProbeSetXRef.`ProbeSetFreezeId`
-        FROM (ProbeSetXRef, ProbeSetFreeze, ProbeFreeze)
-        WHERE ProbeSetXRef.`ProbeSetFreezeId`=ProbeSetFreeze.`Id`
-        AND ProbeSetFreeze.`ProbeFreezeId`=ProbeFreeze.`Id`
-        AND ProbeFreeze.`InbredSetId`=%s
-        AND ProbeSetXRef.`Locus` LIKE %s
-        """
-    cursor.execute(sql, (inbredsetid, locus))
-    return cursor.fetchall()
-
-def get_normalized_probeset(locus, inbredsetid):
-    normalized_probesets = []
-    probesetxrefs = get_probesetxref_inbredsetid(locus, inbredsetid)
-    for probesetxref in probesetxrefs:
-        normalized_probeset = []
-        #
-        probesetfreezeid = probesetxref[4]
-        probesetfreeze = datastructure.get_probesetfreeze(probesetfreezeid)
-        normalized_probeset.append(probesetfreeze[0])
-        normalized_probeset.append(probesetfreeze[1])
-        normalized_probeset.append(probesetfreeze[2])
-        #
-        probesetid = probesetxref[0]
-        probeset = get_probeset(probesetid)
-        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)
-    return normalized_probesets