From db41cd49b6d8ccd2c3318209118ffe098bc9293e Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 19 Aug 2020 03:57:05 +0300
Subject: Remove extra whitespace(or add it) from comma separated items

See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib>
---
 scripts/maintenance/QTL_Reaper_v6.py       |  4 ++--
 scripts/maintenance/readProbeSetMean_v7.py | 28 ++++++++++++++--------------
 2 files changed, 16 insertions(+), 16 deletions(-)

(limited to 'scripts')

diff --git a/scripts/maintenance/QTL_Reaper_v6.py b/scripts/maintenance/QTL_Reaper_v6.py
index 2fbeb53b..35f2d1a1 100755
--- a/scripts/maintenance/QTL_Reaper_v6.py
+++ b/scripts/maintenance/QTL_Reaper_v6.py
@@ -7,7 +7,7 @@ import reaper
 import MySQLdb
 import time
 
-con = MySQLdb.Connect(db='db_webqtl',user='username',passwd='', host="localhost")
+con = MySQLdb.Connect(db='db_webqtl', user='username', passwd='', host="localhost")
 cursor = con.cursor()
 
 genotypeDir = '/gnshare/gn/web/genotypes/'
@@ -102,7 +102,7 @@ for ProbeSetFreezeId in ProbeSetFreezeIds:
 
 		kj += 1
 		if kj%1000==0:
-			print((ProbeSetFreezeId, InbredSets[InbredSetId],kj))
+			print((ProbeSetFreezeId, InbredSets[InbredSetId], kj))
 
 
 	print(ProbeSetFreezeIds)
diff --git a/scripts/maintenance/readProbeSetMean_v7.py b/scripts/maintenance/readProbeSetMean_v7.py
index 864b4e08..59a51cf9 100755
--- a/scripts/maintenance/readProbeSetMean_v7.py
+++ b/scripts/maintenance/readProbeSetMean_v7.py
@@ -39,7 +39,7 @@ 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)
+        con = MySQLdb.Connect(db='db_webqtl', host='localhost', user='username', passwd=passwd)
 
         db = con.cursor()
         print("You have successfully connected to mysql.\n")
@@ -60,14 +60,14 @@ 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 = list(map(string.strip, header))
 nfield = len(header)
 line = fp.readline()
 
 kj=0
 while line:
-	line2 = string.split(string.strip(line),'\t')
+	line2 = string.split(string.strip(line), '\t')
 	line2 = list(map(string.strip, line2))
 	if len(line2) != nfield:
 		print(("Error : " + line))
@@ -78,7 +78,7 @@ while line:
 
 	kj+=1
 	if kj%100000 == 0:
-		print(('checked ',kj,' lines'))
+		print(('checked ', kj, ' lines'))
 
 GeneList = sorted(map(string.lower, GeneList))
 	
@@ -86,7 +86,7 @@ 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
@@ -98,7 +98,7 @@ 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 = list(map(string.strip, header))
 header = list(map(translateAlias, header))
 header = header[dataStart:]
@@ -108,14 +108,14 @@ for item in header:
 		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'))
+		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'))
+print(('used ', time.time()-time0, ' seconds'))
 ########################################################################
 #
 # Check if each ProbeSet exist in database
@@ -126,7 +126,7 @@ 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 = list(map(string.strip, line2))
 PId = line2[0]
 
@@ -185,7 +185,7 @@ if isCont==0:
 	sys.exit(0)
 
 
-print(('used ',time.time()-time0,' seconds'))
+print(('used ', time.time()-time0, ' seconds'))
 #########################################################################
 #
 # Insert data into database
@@ -200,7 +200,7 @@ results = db.fetchall()
 NameIds = {}
 for item in results:
 	NameIds[item[0]] = item[1]
-print(('used ',time.time()-time0,' seconds'))
+print(('used ', time.time()-time0, ' seconds'))
 
 
 print('inserting data')
@@ -220,7 +220,7 @@ kj = 0
 values1 = []
 values2 = []
 while line:
-	line2 = string.split(string.strip(line),'\t')
+	line2 = string.split(string.strip(line), '\t')
 	line2 = list(map(string.strip, line2))
 	PId = line2[0]
 	recordId = NameIds[PId]
@@ -253,8 +253,8 @@ while line:
 
 		values1=[]
 		values2=[]
-		print(('Inserted ', kj,' lines'))
-		print(('used ',time.time()-time0,' seconds'))
+		print(('Inserted ', kj, ' lines'))
+		print(('used ', time.time()-time0, ' seconds'))
 	
 	line = fp.readline()
 
-- 
cgit v1.2.3