diff options
Diffstat (limited to 'scripts/maintenance/readProbeSetSE_v7.py')
| -rwxr-xr-x | scripts/maintenance/readProbeSetSE_v7.py | 254 |
1 files changed, 254 insertions, 0 deletions
diff --git a/scripts/maintenance/readProbeSetSE_v7.py b/scripts/maintenance/readProbeSetSE_v7.py new file mode 100755 index 00000000..fd6f0bb8 --- /dev/null +++ b/scripts/maintenance/readProbeSetSE_v7.py @@ -0,0 +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()
+
+
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