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import sys
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
locus="rs3663871"
inbredsetid=1
results = get_normalized_probeset(locus=locus, inbredsetid=inbredsetid)
file = open('probesets_%s.txt' % (locus), 'w+')
file.write("GN Dataset ID\t")
file.write("Dataset Full Name\t")
file.write("ProbeSet Name\t")
file.write("Symbol\t")
file.write("ProbeSet Description\t")
file.write("Probe Target Description\t")
file.write("ProbeSet Chr\t")
file.write("ProbeSet Mb\t")
file.write("Mean\t")
file.write("LRS\t")
file.write("Geno Chr\t")
file.write("Geno Mb\t")
file.write("\n")
file.flush()
for row in results:
file.write("%s\t" % (row[0]))
file.write("%s\t" % (utilities.clearspaces(row[2], default='')))
file.write("%s\t" % (utilities.clearspaces(row[3], default='')))
file.write("%s\t" % (utilities.clearspaces(row[4], default='')))
file.write("%s\t" % (utilities.clearspaces(row[5], default='')))
file.write("%s\t" % (utilities.clearspaces(row[6], default='')))
file.write("%s\t" % (utilities.clearspaces(row[7], default='')))
file.write("%s\t" % (row[8]))
file.write("%s\t" % (row[9]))
file.write("%s\t" % (row[10]))
file.write("%s\t" % (utilities.clearspaces(row[11], default='')))
file.write("%s\t" % (row[12]))
file.write('\n')
file.flush()
file.close()
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