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-rw-r--r--wqflask/maintenance/dataset/probesets.py90
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