Apply pep8

* scripts/maintenance/readProbeSetSE_v7.py: Apply pep8 to file to replace tabs
with spaces and use correct indentation.

1 files changed, 130 insertions, 128 deletions

diff --git a/scripts/maintenance/readProbeSetSE_v7.py b/scripts/maintenance/readProbeSetSE_v7.py
index fd6f0bb8..2a1d44ff 100755
--- a/scripts/maintenance/readProbeSetSE_v7.py
+++ b/scripts/maintenance/readProbeSetSE_v7.py
@@ -13,12 +13,12 @@ import time
 

 

 def translateAlias(str):

-	if str == "B6":

-		return "C57BL/6J"

-	elif str == "D2":

-		return "DBA/2J"

-	else:

-		return str

+    if str == "B6":

+        return "C57BL/6J"

+    elif str == "D2":

+        return "DBA/2J"

+    else:

+        return str

 

 ########################################################################

 #

@@ -26,25 +26,27 @@ def translateAlias(str):
 #

 ########################################################################

 

+

 dataStart = 1

 

-GeneChipId = int( raw_input("Enter GeneChipId:") )

-ProbeSetFreezeId = int( raw_input("Enter ProbeSetFreezeId:") )

+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)

+    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"

+    db = con.cursor()

+    print("You have successfully connected to mysql.\n")

 except:

-	print "You entered incorrect password.\n"

-        sys.exit(0)

-	

+    print("You entered incorrect password.\n")

+    sys.exit(0)

+

 time0 = time.time()

 ########################################################################

 #

@@ -52,9 +54,9 @@ time0 = time.time()
 #

 ########################################################################

 

-#GeneChipId = 4 

-#dataStart = 1 	

-#ProbeSetFreezeId = 359 #JAX Liver 6C Affy M430 2.0 (Jul11) MDP

+#GeneChipId = 4

+#dataStart = 1

+# ProbeSetFreezeId = 359 #JAX Liver 6C Affy M430 2.0 (Jul11) MDP

 #fp = open("GSE10493_AllSamples_6C_Z_AvgSE.txt", 'rb')

 

 

@@ -64,191 +66,191 @@ time0 = time.time()
 #  generate the gene list of expression data here

 #

 #########################################################################

-print 'Checking if each line have same number of members'

+print('Checking if each line have same number of members')

 

 GeneList = []

 isCont = 1

 header = fp.readline()

-header = string.split(string.strip(header),'\t')

+header = string.split(string.strip(header), '\t')

 header = map(string.strip, header)

 nfield = len(header)

 line = fp.readline()

 

-kj=0

+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

+    line2 = string.split(string.strip(line), '\t')

+    line2 = map(string.strip, line2)

+    if len(line2) != nfield:

+        isCont = 0

+        print("Error : " + line)

 

-	GeneList.append(line2[0])

-	line = fp.readline()

+    GeneList.append(line2[0])

+    line = fp.readline()

 

-	kj+=1

-	if kj%100000 == 0:

-		print 'checked ',kj,' lines'

+    kj += 1

+    if kj % 100000 == 0:

+        print('checked ', kj, ' lines')

 

 GeneList = map(string.lower, GeneList)

 GeneList.sort()

-	

-if isCont==0:

-	sys.exit(0)

 

+if isCont == 0:

+    sys.exit(0)

 

-print 'used ',time.time()-time0,' seconds'

+

+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'

+print('Checking if each strain exist in database')

 

 isCont = 1

 fp.seek(0)

 header = fp.readline()

-header = string.split(string.strip(header),'\t')

+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

+    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)

+if isCont == 0:

+    sys.exit(0)

 

 

-print 'used ',time.time()-time0,' seconds'

+print('used ', time.time()-time0, ' seconds')

 ########################################################################

 #

 # Check if each ProbeSet exist in database

 #

 ########################################################################

-print '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 = 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))

+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'

+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))

+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 --#

+    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

+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)

+    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'

+print('used ', time.time()-time0, ' seconds')

 #############################

-#Insert new Data into SE

+# 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))

+        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

+    ProbeNameId[Name] = Id

 

 ferror = open("ProbeError.txt", "wb")

 

 DataValues = []

 

-fp.seek(0) #XZ add this line

-line = fp.readline() #XZ add this line

+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)

+    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")

+    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()

-

-