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authorPjotr Prins2018-04-03 07:50:28 +0000
committerPjotr Prins2018-04-03 07:50:28 +0000
commitfb57f05083b0512b7bb9f9e15b6cc6efaded5a1f (patch)
treeb2d5e7cf8f9a52a44b719103809276315de7f325 /scripts/maintenance/QTL_Reaper_v6.py
parent9544ca2e6461b267c28d9a4c7fe976bc34f10be3 (diff)
downloadgenenetwork2-fb57f05083b0512b7bb9f9e15b6cc6efaded5a1f.tar.gz
@acenteno added data upload scripts into main repo
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diff --git a/scripts/maintenance/QTL_Reaper_v6.py b/scripts/maintenance/QTL_Reaper_v6.py
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+####### To run this program do: python QTL_Reaper_v2.py 235
+#Where 163 is the ProbeSetFreeze Id of the database that we want to calculate #the LRS
+#!/usr/bin/python
+import sys
+import os
+import reaper
+import MySQLdb
+import time
+
+con = MySQLdb.Connect(db='db_webqtl',user='username',passwd='', host="localhost")
+cursor = con.cursor()
+
+genotypeDir = '/gnshare/gn/web/genotypes/'
+genotype_1 = reaper.Dataset()
+
+#####get all of the genotypes
+cursor.execute('select Id, Name from InbredSet')
+results = cursor.fetchall()
+InbredSets = {}
+for item in results:
+ InbredSets[item[0]] = genotypeDir+str(item[1])+'.geno'
+
+ProbeSetFreezeIds=sys.argv[1:]
+if ProbeSetFreezeIds:
+ #####convert the Ids to integer
+ ProbeSetFreezeIds=map(int, ProbeSetFreezeIds)
+
+else:
+ #####get all of the dataset that need be updated
+ cursor.execute('select distinct(ProbeSetFreezeId) from ProbeSetXRef where pValue is NULL order by ProbeSetFreezeId desc')
+ results = cursor.fetchall()
+ ProbeSetFreezeIds = []
+ for item in results:
+ ProbeSetFreezeIds.append(item[0])
+
+####human dataset can NOT use this program calculate the LRS, ignore it
+if ProbeSetFreezeIds.__contains__(215):
+ ProbeSetFreezeIds.remove(215)
+
+#output_file = open ('/home/xzhou/work/DatabaseTools/cal_LRS_Additive_result.txt', 'w')
+
+#####update
+for ProbeSetFreezeId in ProbeSetFreezeIds:
+ cursor.execute("""
+ select InbredSetId
+ from ProbeFreeze, ProbeSetFreeze
+ where ProbeFreeze.Id=ProbeSetFreeze.ProbeFreezeId and ProbeSetFreeze.Id=%d
+ """%ProbeSetFreezeId);
+
+ InbredSetId = cursor.fetchone()[0]
+ if InbredSetId==3:
+ InbredSetId=1
+ #if InbredSetId==12:
+ # InbredSetId=2
+
+ print ProbeSetFreezeId, InbredSets[InbredSetId]
+
+ genotype_1.read(InbredSets[InbredSetId])
+ locuses = []
+ for geno in genotype_1:
+ for locus in geno:
+ locuses.append(locus.name)
+
+ cursor.execute('select ProbeSetId, Locus, DataId from ProbeSetXRef where ProbeSetFreezeId=%s'%ProbeSetFreezeId)
+ ProbeSetXRefInfos = cursor.fetchall()
+
+ kj=0
+ for aProbeSetXRef in ProbeSetXRefInfos:
+ ProbeSetId, Locus, DataId = aProbeSetXRef
+ prgy = genotype_1.prgy
+
+ cursor.execute("select Strain.Name, ProbeSetData.value from Strain, ProbeSetData where Strain.Id = ProbeSetData.StrainId and ProbeSetData.Id = %d" % DataId)
+ results = cursor.fetchall()
+ if not results:
+ continue
+ _strains = []
+ _values = []
+ for item2 in results:
+ strain, value = item2
+ if strain in prgy:
+ _strains.append(strain)
+ _values.append(value)
+ if not _strains or not _values:
+ continue
+
+ if len(_strains) < 8:
+ continue
+ qtlresults = genotype_1.regression(strains = _strains, trait = _values)
+ _max = max(qtlresults)
+ _locus = _max.locus.name
+ _additive = _max.additive
+ _max = _max.lrs
+
+ #output_file.write('%s\t%s\t%s\t%s\t%s\n' % (ProbeSetFreezeId, ProbeSetId, _locus, _max, _additive))
+
+ # _max(LRS) maybe is infinite sometimes, so define it as a very big number
+ if _max == float('inf'):
+ _max = 10000
+
+ cursor.execute('update ProbeSetXRef set Locus=%s, LRS=%s, additive=%s where ProbeSetId=%s and ProbeSetFreezeId=%s', \
+ (_locus, _max, _additive, ProbeSetId, ProbeSetFreezeId))
+
+ kj += 1
+ if kj%1000==0:
+ print ProbeSetFreezeId, InbredSets[InbredSetId],kj
+
+
+ print ProbeSetFreezeIds