Merge pull request #1 from genenetwork/testing

Updating my testing branch

1 files changed, 274 insertions, 0 deletions

diff --git a/scripts/maintenance/readProbeSetMean_v7.py b/scripts/maintenance/readProbeSetMean_v7.py
new file mode 100755
index 00000000..e9c8f25c
--- /dev/null
+++ b/scripts/maintenance/readProbeSetMean_v7.py
@@ -0,0 +1,274 @@
+#!/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
+########################################################################
+import string
+import sys
+import MySQLdb
+import getpass
+import time
+#import pdb
+
+#pdb.set_trace()
+
+########################################################################
+
+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()
+
+#########################################################################
+#
+#  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])
+	
+print Names
+
+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, check if the ProbeSet name is correct"
+	isCont = 0
+        
+if isCont==0:
+	sys.exit(0)
+
+
+print 'used ',time.time()-time0,' seconds'
+#########################################################################
+#
+# Insert data into database
+#
+#########################################################################
+print 'getting ProbeSet/Id'
+
+
+#---- get Name/Id map ----#
+db.execute('select %s, Id from ProbeSet where ChipId=%d order by %s' % (IdStr, GeneChipId, IdStr))
+results = db.fetchall()
+NameIds = {}
+for item in results:
+	NameIds[item[0]] = item[1]
+print 'used ',time.time()-time0,' seconds'
+
+
+print 'inserting data'
+
+##---- get old max dataId ----##
+db.execute('select max(Id) from ProbeSetData')
+maxDataId = int(db.fetchall()[0][0])
+bmax = maxDataId
+print "old_max = %d\n" % bmax
+
+##---- insert data ----##
+fp.seek(0)
+line = fp.readline()
+line = fp.readline()
+kj = 0
+
+values1 = []
+values2 = []
+while line:
+	line2 = string.split(string.strip(line),'\t')
+	line2 = map(string.strip, line2)
+	PId = line2[0]
+	recordId = NameIds[PId]
+
+	maxDataId += 1
+	datasorig = line2[dataStart:]
+	
+	###### Data Table items ######
+	i=0
+	for item in datasorig:
+		try:
+			values1.append('(%d,%d,%s)' % (maxDataId, Ids[i], float(item)))
+      		except:
+			pass
+		i += 1
+
+	values2.append("(%d,%d,%d)" % (ProbeSetFreezeId, recordId, maxDataId))
+
+
+	##---- insert into table ----##
+	kj += 1
+	if kj % 100 == 0:
+		cmd = ','.join(values1)
+		cmd = 'insert into ProbeSetData values %s' % cmd
+		db.execute(cmd)
+
+		cmd = ','.join(values2)
+		cmd = 'insert into ProbeSetXRef(ProbeSetFreezeId, ProbeSetId, DataId) values %s' % cmd
+		db.execute(cmd)
+
+		values1=[]
+		values2=[]
+		print 'Inserted ', kj,' lines'
+		print 'used ',time.time()-time0,' seconds'
+	
+	line = fp.readline()
+
+
+
+if len(values1)>0:
+	cmd = ','.join(values1)
+	cmd = 'insert into ProbeSetData values %s' % cmd
+	db.execute(cmd)
+
+	cmd = ','.join(values2)
+	cmd = 'insert into ProbeSetXRef(ProbeSetFreezeId, ProbeSetId, DataId) values %s' % cmd
+	db.execute(cmd)
+
+con.close()