Merge github.com:genenetwork/genenetwork2 into acenteno

1 files changed, 254 insertions, 254 deletions

diff --git a/scripts/maintenance/readProbeSetSE_v7.py b/scripts/maintenance/readProbeSetSE_v7.py
index fd6f0bb8..2cfe2e07 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 = [item.strip() for item in header]
+nfield = len(header)
+line = fp.readline()
+
+kj = 0
+while line:
+    line2 = line.strip().split('\t')
+    line2 = [item.strip() for item in 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 = [item.strip() for item in 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()