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-rwxr-xr-xscripts/maintenance/readProbeSetSE_v7.py508
1 files changed, 254 insertions, 254 deletions
diff --git a/scripts/maintenance/readProbeSetSE_v7.py b/scripts/maintenance/readProbeSetSE_v7.py
index fd6f0bb8..edd9e7b0 100755
--- a/scripts/maintenance/readProbeSetSE_v7.py
+++ b/scripts/maintenance/readProbeSetSE_v7.py
@@ -1,254 +1,254 @@
-#!/usr/bin/python2
-"""This script use the nearest marker to the transcript as control, increasing permutation rounds according to the p-value"""
-########################################################################
-# Last Updated Sep 27, 2011 by Xiaodong
-# This version fix the bug that incorrectly exclude the first 2 probesetIDs
-########################################################################
-
-import string
-import sys
-import MySQLdb
-import getpass
-import time
-
-
-def translateAlias(str):
- if str == "B6":
- return "C57BL/6J"
- elif str == "D2":
- return "DBA/2J"
- else:
- return str
-
-########################################################################
-#
-# Indicate Data Start Position, ProbeFreezeId, GeneChipId, DataFile
-#
-########################################################################
-
-dataStart = 1
-
-GeneChipId = int( raw_input("Enter GeneChipId:") )
-ProbeSetFreezeId = int( raw_input("Enter ProbeSetFreezeId:") )
-input_file_name = raw_input("Enter file name with suffix:")
-
-fp = open("%s" % input_file_name, 'rb')
-
-
-try:
- passwd = getpass.getpass('Please enter mysql password here : ')
- con = MySQLdb.Connect(db='db_webqtl',host='localhost', user='username',passwd=passwd)
-
- db = con.cursor()
- print "You have successfully connected to mysql.\n"
-except:
- print "You entered incorrect password.\n"
- sys.exit(0)
-
-time0 = time.time()
-########################################################################
-#
-# Indicate Data Start Position, ProbeFreezeId, GeneChipId, DataFile
-#
-########################################################################
-
-#GeneChipId = 4
-#dataStart = 1
-#ProbeSetFreezeId = 359 #JAX Liver 6C Affy M430 2.0 (Jul11) MDP
-#fp = open("GSE10493_AllSamples_6C_Z_AvgSE.txt", 'rb')
-
-
-#########################################################################
-#
-# Check if each line have same number of members
-# generate the gene list of expression data here
-#
-#########################################################################
-print 'Checking if each line have same number of members'
-
-GeneList = []
-isCont = 1
-header = fp.readline()
-header = string.split(string.strip(header),'\t')
-header = map(string.strip, header)
-nfield = len(header)
-line = fp.readline()
-
-kj=0
-while line:
- line2 = string.split(string.strip(line),'\t')
- line2 = map(string.strip, line2)
- if len(line2) != nfield:
- print "Error : " + line
- isCont = 0
-
- GeneList.append(line2[0])
- line = fp.readline()
-
- kj+=1
- if kj%100000 == 0:
- print 'checked ',kj,' lines'
-
-GeneList = map(string.lower, GeneList)
-GeneList.sort()
-
-if isCont==0:
- sys.exit(0)
-
-
-print 'used ',time.time()-time0,' seconds'
-#########################################################################
-#
-# Check if each strain exist in database
-# generate the string id list of expression data here
-#
-#########################################################################
-print 'Checking if each strain exist in database'
-
-isCont = 1
-fp.seek(0)
-header = fp.readline()
-header = string.split(string.strip(header),'\t')
-header = map(string.strip, header)
-header = map(translateAlias, header)
-header = header[dataStart:]
-Ids = []
-for item in header:
- try:
- db.execute('select Id from Strain where Name = "%s"' % item)
- Ids.append(db.fetchall()[0][0])
- except:
- print item,'does not exist, check the if the strain name is correct'
- isCont=0
-
-if isCont==0:
- sys.exit(0)
-
-
-print 'used ',time.time()-time0,' seconds'
-########################################################################
-#
-# Check if each ProbeSet exist in database
-#
-########################################################################
-print 'Check if each ProbeSet exist in database'
-
-##---- find PID is name or target ----##
-line = fp.readline()
-line = fp.readline()
-line2 = string.split(string.strip(line),'\t')
-line2 = map(string.strip, line2)
-PId = line2[0]
-
-db.execute('select Id from ProbeSet where Name="%s" and ChipId=%d' % (PId, GeneChipId))
-results = db.fetchall()
-IdStr = 'TargetId'
-if len(results)>0:
- IdStr = 'Name'
-
-
-##---- get Name/TargetId list from database ----##
-db.execute('select distinct(%s) from ProbeSet where ChipId=%d order by %s' % (IdStr, GeneChipId, IdStr))
-results = db.fetchall()
-
-Names = []
-for item in results:
- Names.append(item[0])
-Names = map(string.lower, Names)
-Names.sort() # -- Fixed the lower case problem of ProbeSets affx-mur_b2_at doesn't exist --#
-
-##---- compare genelist with names ----##
-x=y=0
-x1=-1
-GeneList2=[]
-while x<len(GeneList) and y<len(Names):
- if GeneList[x]==Names[y]:
- x += 1
- y += 1
- elif GeneList[x]<Names[y]:
- if x!=x1:
- GeneList2.append(GeneList[x])
- x1 = x
- x += 1
- elif GeneList[x]>Names[y]:
- y += 1
-
- if x%100000==0:
- print 'check Name, checked %d lines'%x
-
-while x<len(GeneList):
- GeneList2.append(GeneList[x])
- x += 1
-
-isCont=1
-ferror = open("ProbeSetError.txt", "wb")
-for item in GeneList2:
- ferror.write(item + " doesn't exist \n")
- print item, " doesn't exist"
- isCont = 0
-
-if isCont==0:
- sys.exit(0)
-
-
-print 'used ',time.time()-time0,' seconds'
-#############################
-#Insert new Data into SE
-############################
-db.execute("""
- select ProbeSet.%s, ProbeSetXRef.DataId from ProbeSet, ProbeSetXRef
- where ProbeSet.Id=ProbeSetXRef.ProbeSetId and ProbeSetXRef.ProbeSetFreezeId=%d"""
- % (IdStr, ProbeSetFreezeId))
-results = db.fetchall()
-
-ProbeNameId = {}
-for Name, Id in results:
- ProbeNameId[Name] = Id
-
-ferror = open("ProbeError.txt", "wb")
-
-DataValues = []
-
-fp.seek(0) #XZ add this line
-line = fp.readline() #XZ add this line
-line = fp.readline()
-
-kj = 0
-while line:
- line2 = string.split(string.strip(line),'\t')
- line2 = map(string.strip, line2)
-
- CellId = line2[0]
- if not ProbeNameId.has_key(CellId):
- ferror.write(CellId + " doesn't exist\n")
- print CellId, " doesn't exist"
- else:
- DataId = ProbeNameId[CellId]
- datasorig = line2[dataStart:]
-
- i = 0
- for item in datasorig:
- if item != '':
- value = '('+str(DataId)+','+str(Ids[i])+','+str(item)+')'
- DataValues.append(value)
- i += 1
-
- kj += 1
- if kj % 100 == 0:
- Dataitems = ','.join(DataValues)
- cmd = 'insert ProbeSetSE values %s' % Dataitems
- db.execute(cmd)
-
- DataValues = []
- print 'inserted ',kj,' lines'
- print 'used ',time.time()-time0,' seconds'
- line = fp.readline()
-
-if len(DataValues)>0:
- DataValues = ','.join(DataValues)
- cmd = 'insert ProbeSetSE values %s' % DataValues
- db.execute(cmd)
-
-con.close()
-
-
+#!/usr/bin/python2
+"""This script use the nearest marker to the transcript as control, increasing permutation rounds according to the p-value"""
+########################################################################
+# Last Updated Sep 27, 2011 by Xiaodong
+# This version fix the bug that incorrectly exclude the first 2 probesetIDs
+########################################################################
+
+import string
+import sys
+import MySQLdb
+import getpass
+import time
+
+
+def translateAlias(str):
+ if str == "B6":
+ return "C57BL/6J"
+ elif str == "D2":
+ return "DBA/2J"
+ else:
+ return str
+
+########################################################################
+#
+# Indicate Data Start Position, ProbeFreezeId, GeneChipId, DataFile
+#
+########################################################################
+
+
+dataStart = 1
+
+GeneChipId = int(input("Enter GeneChipId:"))
+ProbeSetFreezeId = int(input("Enter ProbeSetFreezeId:"))
+input_file_name = input("Enter file name with suffix:")
+
+fp = open("%s" % input_file_name, 'rb')
+
+
+try:
+ passwd = getpass.getpass('Please enter mysql password here : ')
+ con = MySQLdb.Connect(db='db_webqtl', host='localhost',
+ user='username', passwd=passwd)
+
+ db = con.cursor()
+ print("You have successfully connected to mysql.\n")
+except:
+ print("You entered incorrect password.\n")
+ sys.exit(0)
+
+time0 = time.time()
+########################################################################
+#
+# Indicate Data Start Position, ProbeFreezeId, GeneChipId, DataFile
+#
+########################################################################
+
+#GeneChipId = 4
+#dataStart = 1
+# ProbeSetFreezeId = 359 #JAX Liver 6C Affy M430 2.0 (Jul11) MDP
+#fp = open("GSE10493_AllSamples_6C_Z_AvgSE.txt", 'rb')
+
+
+#########################################################################
+#
+# Check if each line have same number of members
+# generate the gene list of expression data here
+#
+#########################################################################
+print('Checking if each line have same number of members')
+
+GeneList = []
+isCont = 1
+header = fp.readline()
+header = header.strip().split('\t')
+header = list(map(string.strip, header))
+nfield = len(header)
+line = fp.readline()
+
+kj = 0
+while line:
+ line2 = line.strip().split('\t')
+ line2 = list(map(string.strip, line2))
+ if len(line2) != nfield:
+ isCont = 0
+ print(("Error : " + line))
+
+ GeneList.append(line2[0])
+ line = fp.readline()
+
+ kj += 1
+ if kj % 100000 == 0:
+ print(('checked ', kj, ' lines'))
+
+GeneList = sorted(map(string.lower, GeneList))
+
+if isCont == 0:
+ sys.exit(0)
+
+
+print(('used ', time.time()-time0, ' seconds'))
+#########################################################################
+#
+# Check if each strain exist in database
+# generate the string id list of expression data here
+#
+#########################################################################
+print('Checking if each strain exist in database')
+
+isCont = 1
+fp.seek(0)
+header = fp.readline()
+header = header.strip().split('\t')
+header = list(map(string.strip, header))
+header = list(map(translateAlias, header))
+header = header[dataStart:]
+Ids = []
+for item in header:
+ try:
+ db.execute('select Id from Strain where Name = "%s"' % item)
+ Ids.append(db.fetchall()[0][0])
+ except:
+ isCont = 0
+ print((item, 'does not exist, check the if the strain name is correct'))
+
+if isCont == 0:
+ sys.exit(0)
+
+
+print(('used ', time.time()-time0, ' seconds'))
+########################################################################
+#
+# Check if each ProbeSet exist in database
+#
+########################################################################
+print('Check if each ProbeSet exist in database')
+
+##---- find PID is name or target ----##
+line = fp.readline()
+line = fp.readline()
+line2 = line.strip().split('\t')
+line2 = [x.strip() for x in line2]
+PId = line2[0]
+
+db.execute('select Id from ProbeSet where Name="%s" and ChipId=%d' %
+ (PId, GeneChipId))
+results = db.fetchall()
+IdStr = 'TargetId'
+if len(results) > 0:
+ IdStr = 'Name'
+
+
+##---- get Name/TargetId list from database ----##
+db.execute('select distinct(%s) from ProbeSet where ChipId=%d order by %s' % (
+ IdStr, GeneChipId, IdStr))
+results = db.fetchall()
+
+Names = []
+for item in results:
+ Names.append(item[0])
+ Names = sorted(map(string.lower, Names))
+
+##---- compare genelist with names ----##
+x = y = 0
+x1 = -1
+GeneList2 = []
+while x < len(GeneList) and y < len(Names):
+ if GeneList[x] == Names[y]:
+ x += 1
+ y += 1
+ elif GeneList[x] < Names[y]:
+ if x != x1:
+ GeneList2.append(GeneList[x])
+ x1 = x
+ x += 1
+ elif GeneList[x] > Names[y]:
+ y += 1
+
+ if x % 100000 == 0:
+ print(('check Name, checked %d lines' % x))
+
+while x < len(GeneList):
+ GeneList2.append(GeneList[x])
+ x += 1
+
+isCont = 1
+ferror = open("ProbeSetError.txt", "wb")
+for item in GeneList2:
+ ferror.write(item + " doesn't exist \n")
+ isCont = 0
+
+ print((item, " doesn't exist"))
+if isCont == 0:
+ sys.exit(0)
+
+
+print(('used ', time.time()-time0, ' seconds'))
+#############################
+# Insert new Data into SE
+############################
+db.execute("""
+ select ProbeSet.%s, ProbeSetXRef.DataId from ProbeSet, ProbeSetXRef
+ where ProbeSet.Id=ProbeSetXRef.ProbeSetId and ProbeSetXRef.ProbeSetFreezeId=%d"""
+ % (IdStr, ProbeSetFreezeId))
+results = db.fetchall()
+
+ProbeNameId = {}
+for Name, Id in results:
+ ProbeNameId[Name] = Id
+
+ferror = open("ProbeError.txt", "wb")
+
+DataValues = []
+
+fp.seek(0) # XZ add this line
+line = fp.readline() # XZ add this line
+line = fp.readline()
+
+kj = 0
+while line:
+ line2 = line.strip().split('\t')
+ line2 = [x.strip() for x in line2]
+
+ CellId = line2[0]
+ if CellId not in ProbeNameId:
+ ferror.write(CellId + " doesn't exist\n")
+ else:
+ DataId = ProbeNameId[CellId]
+ datasorig = line2[dataStart:]
+
+ i = 0
+ for item in datasorig:
+ if item != '':
+ value = '('+str(DataId)+','+str(Ids[i])+','+str(item)+')'
+ DataValues.append(value)
+ i += 1
+
+ kj += 1
+ if kj % 100 == 0:
+ Dataitems = ','.join(DataValues)
+ cmd = 'insert ProbeSetSE values %s' % Dataitems
+ db.execute(cmd)
+
+ DataValues = []
+ line = fp.readline()
+ print((CellId, " doesn't exist"))
+ print(('inserted ', kj, ' lines'))
+ print(('used ', time.time()-time0, ' seconds'))
+
+if len(DataValues) > 0:
+ DataValues = ','.join(DataValues)
+ cmd = 'insert ProbeSetSE values %s' % DataValues
+ db.execute(cmd)
+
+con.close()
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