Wrap print statements in parentheses

8 files changed, 72 insertions, 72 deletions

diff --git a/scripts/maintenance/QTL_Reaper_v6.py b/scripts/maintenance/QTL_Reaper_v6.py
index e50dbd40..7fb56eca 100755
--- a/scripts/maintenance/QTL_Reaper_v6.py
+++ b/scripts/maintenance/QTL_Reaper_v6.py
@@ -53,7 +53,7 @@ for ProbeSetFreezeId in ProbeSetFreezeIds:
 	#if InbredSetId==12:
 	#	InbredSetId=2
 
-	print ProbeSetFreezeId, InbredSets[InbredSetId]
+	print((ProbeSetFreezeId, InbredSets[InbredSetId]))
 
 	genotype_1.read(InbredSets[InbredSetId])
 	locuses = []
@@ -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
+	print(ProbeSetFreezeIds)
diff --git a/scripts/maintenance/Update_Case_Attributes_MySQL_tab.py b/scripts/maintenance/Update_Case_Attributes_MySQL_tab.py
index 0f8602c9..bf796df4 100644
--- a/scripts/maintenance/Update_Case_Attributes_MySQL_tab.py
+++ b/scripts/maintenance/Update_Case_Attributes_MySQL_tab.py
@@ -24,4 +24,4 @@ for row in csv_data:
 #close the connection to the database.
 mydb.commit()
 cursor.close()
-print "Done"
\ No newline at end of file
+print("Done")
\ No newline at end of file
diff --git a/scripts/maintenance/delete_genotypes.py b/scripts/maintenance/delete_genotypes.py
index fa693f0f..060640e1 100755
--- a/scripts/maintenance/delete_genotypes.py
+++ b/scripts/maintenance/delete_genotypes.py
@@ -8,13 +8,13 @@ import genotypes
 def main(argv):
     # config
     config = utilities.get_config(argv[1])
-    print "config:"
+    print("config:")
     for item in config.items('config'):
-        print "\t%s" % (str(item))
+        print(("\t%s" % (str(item))))
     # var
-    print "variable:"
+    print("variable:")
     inbredsetid = config.get('config', 'inbredsetid')
-    print "\tinbredsetid: %s" % inbredsetid
+    print(("\tinbredsetid: %s" % inbredsetid))
     # datafile
     datafile = open(config.get('config', 'datafile'), 'r')
     datafile = csv.reader(datafile, delimiter='\t', quotechar='"')
@@ -25,9 +25,9 @@ def main(argv):
             continue
         genoname = row[0]
         delrowcount += genotypes.delete(genoname, inbredsetid)
-    print "deleted %d genotypes" % (delrowcount)
+    print(("deleted %d genotypes" % (delrowcount)))
 
 if __name__ == "__main__":
-    print "command line arguments:\n\t%s" % sys.argv
+    print(("command line arguments:\n\t%s" % sys.argv))
     main(sys.argv)
-    print "exit successfully"
+    print("exit successfully")
diff --git a/scripts/maintenance/delete_phenotypes.py b/scripts/maintenance/delete_phenotypes.py
index 326c466e..60dbec61 100755
--- a/scripts/maintenance/delete_phenotypes.py
+++ b/scripts/maintenance/delete_phenotypes.py
@@ -8,13 +8,13 @@ import phenotypes
 def main(argv):
     # config
     config = utilities.get_config(argv[1])
-    print "config:"
+    print("config:")
     for item in config.items('config'):
-        print "\t%s" % (str(item))
+        print(("\t%s" % (str(item))))
     # var
-    print "variable:"
+    print("variable:")
     inbredsetid = config.get('config', 'inbredsetid')
-    print "\tinbredsetid: %s" % inbredsetid
+    print(("\tinbredsetid: %s" % inbredsetid))
     # datafile
     datafile = open(config.get('config', 'datafile'), 'r')
     datafile = csv.reader(datafile, delimiter='\t', quotechar='"')
@@ -27,9 +27,9 @@ def main(argv):
         except:
             continue
         delrowcount += phenotypes.delete(publishxrefid=publishxrefid, inbredsetid=inbredsetid)
-    print "deleted %d phenotypes" % (delrowcount)
+    print(("deleted %d phenotypes" % (delrowcount)))
 
 if __name__ == "__main__":
-    print "command line arguments:\n\t%s" % sys.argv
+    print(("command line arguments:\n\t%s" % sys.argv))
     main(sys.argv)
-    print "exit successfully"
+    print("exit successfully")
diff --git a/scripts/maintenance/load_genotypes.py b/scripts/maintenance/load_genotypes.py
index 338483f4..c235a31f 100755
--- a/scripts/maintenance/load_genotypes.py
+++ b/scripts/maintenance/load_genotypes.py
@@ -8,7 +8,7 @@ def main(argv):
     config = utilities.get_config(argv[1])
     print("config file:")
     for item in config.items('config'):
-        print("\t%s" % str(item))
+        print(("\t%s" % str(item)))
     parse_genofile(config, fetch_parameters(config))
 
 def fetch_parameters(config):
@@ -20,7 +20,7 @@ def fetch_parameters(config):
     config_dic['genofile'] = config.get('config', 'genofile')
     print("config dictionary:")
     for k, v in config_dic.items():
-        print("\t%s: %s" % (k, v))
+        print(("\t%s: %s" % (k, v)))
     return config_dic
 
 def parse_genofile(config, config_dic):
@@ -43,9 +43,9 @@ def parse_genofile(config, config_dic):
             #
             print("geno file meta dictionary:")
             for k, v in meta_dic.items():
-                print("\t%s: %s" % (k, v))
+                print(("\t%s: %s" % (k, v)))
             #
-            print("geno file head:\n\t%s" % line)
+            print(("geno file head:\n\t%s" % line))
             strainnames = line.split()[4:]
             config_dic['strains'] = datastructure.get_strains_bynames(inbredsetid=config_dic['inbredsetid'], strainnames=strainnames, updatestrainxref="yes")
             continue
@@ -81,7 +81,7 @@ def check_or_insert_geno(config_dic, marker_dic):
     result = cursor.fetchone()
     if result:
         genoid = result[0]
-        print("get geno record: %d" % genoid)
+        print(("get geno record: %d" % genoid))
     else:
         sql = """
             INSERT INTO Geno
@@ -95,7 +95,7 @@ def check_or_insert_geno(config_dic, marker_dic):
         cursor.execute(sql, (config_dic['speciesid'], marker_dic['locus'], marker_dic['locus'], marker_dic['chromosome'], marker_dic['mb']))
         rowcount = cursor.rowcount
         genoid = con.insert_id()
-        print("INSERT INTO Geno: %d record: %d" % (rowcount, genoid))
+        print(("INSERT INTO Geno: %d record: %d" % (rowcount, genoid)))
     return genoid
 
 def check_genoxref(config_dic, marker_dic):
@@ -146,9 +146,9 @@ def insert_genoxref(config_dic, marker_dic):
         """
     cursor.execute(sql, (config_dic['genofreezeid'], marker_dic['genoid'], config_dic['dataid'], marker_dic['cm'], 'N'))
     rowcount = cursor.rowcount
-    print("INSERT INTO GenoXRef: %d record" % (rowcount))
+    print(("INSERT INTO GenoXRef: %d record" % (rowcount)))
 
 if __name__ == "__main__":
-    print("command line arguments:\n\t%s" % sys.argv)
+    print(("command line arguments:\n\t%s" % sys.argv))
     main(sys.argv)
     print("exit successfully")
diff --git a/scripts/maintenance/load_phenotypes.py b/scripts/maintenance/load_phenotypes.py
index c3c6570b..61d527d4 100755
--- a/scripts/maintenance/load_phenotypes.py
+++ b/scripts/maintenance/load_phenotypes.py
@@ -7,31 +7,31 @@ import datastructure
 def main(argv):
     # config
     config = utilities.get_config(argv[1])
-    print "config:"
+    print("config:")
     for item in config.items('config'):
-        print "\t%s" % (str(item))
+        print(("\t%s" % (str(item))))
     # var
     inbredsetid = config.get('config', 'inbredsetid')
-    print "inbredsetid: %s" % inbredsetid
+    print(("inbredsetid: %s" % inbredsetid))
     species = datastructure.get_species(inbredsetid)
     speciesid = species[0]
-    print "speciesid: %s" % speciesid
+    print(("speciesid: %s" % speciesid))
     dataid = datastructure.get_nextdataid_phenotype()
-    print "next data id: %s" % dataid
+    print(("next data id: %s" % dataid))
     cursor, con = utilities.get_cursor()
     # datafile
     datafile = open(config.get('config', 'datafile'), 'r')
     phenotypedata = csv.reader(datafile, delimiter='\t', quotechar='"')
     phenotypedata_head = phenotypedata.next()
-    print "phenotypedata head:\n\t%s" % phenotypedata_head
+    print(("phenotypedata head:\n\t%s" % phenotypedata_head))
     strainnames = phenotypedata_head[1:]
     strains = datastructure.get_strains_bynames(inbredsetid=inbredsetid, strainnames=strainnames, updatestrainxref="yes")
     # metafile
     metafile = open(config.get('config', 'metafile'), 'r')
     phenotypemeta = csv.reader(metafile, delimiter='\t', quotechar='"')
     phenotypemeta_head = phenotypemeta.next()
-    print "phenotypemeta head:\n\t%s" % phenotypemeta_head
-    print
+    print(("phenotypemeta head:\n\t%s" % phenotypemeta_head))
+    print()
     # load
     for metarow in phenotypemeta:
         #
@@ -67,7 +67,7 @@ def main(argv):
             ))
         rowcount = cursor.rowcount
         phenotypeid = con.insert_id()
-        print "INSERT INTO Phenotype: %d record: %d" % (rowcount, phenotypeid)
+        print(("INSERT INTO Phenotype: %d record: %d" % (rowcount, phenotypeid)))
         # Publication
         publicationid = None # reset
         pubmed_id = utilities.to_db_string(metarow[0], None)
@@ -81,7 +81,7 @@ def main(argv):
             re = cursor.fetchone()
             if re:
                 publicationid = re[0]
-                print "get Publication record: %d" % publicationid
+                print(("get Publication record: %d" % publicationid))
         if not publicationid:
             sql = """
                 INSERT INTO Publication
@@ -109,7 +109,7 @@ def main(argv):
                 ))
             rowcount = cursor.rowcount
             publicationid = con.insert_id()
-            print "INSERT INTO Publication: %d record: %d" % (rowcount, publicationid)
+            print(("INSERT INTO Publication: %d record: %d" % (rowcount, publicationid)))
         # data
         for index, strain in enumerate(strains):
             #
@@ -158,14 +158,14 @@ def main(argv):
         cursor.execute(sql, (inbredsetid, phenotypeid, publicationid, dataid, ""))
         rowcount = cursor.rowcount
         publishxrefid = con.insert_id()
-        print "INSERT INTO PublishXRef: %d record: %d" % (rowcount, publishxrefid)
+        print(("INSERT INTO PublishXRef: %d record: %d" % (rowcount, publishxrefid)))
         # for loop next
         dataid += 1
-        print
+        print()
     # release
     con.close()
 
 if __name__ == "__main__":
-    print "command line arguments:\n\t%s" % sys.argv
+    print(("command line arguments:\n\t%s" % sys.argv))
     main(sys.argv)
-    print "exit successfully"
+    print("exit successfully")
diff --git a/scripts/maintenance/readProbeSetMean_v7.py b/scripts/maintenance/readProbeSetMean_v7.py
index e9c8f25c..e7a4c826 100755
--- a/scripts/maintenance/readProbeSetMean_v7.py
+++ b/scripts/maintenance/readProbeSetMean_v7.py
@@ -42,9 +42,9 @@ try:
         con = MySQLdb.Connect(db='db_webqtl',host='localhost', user='username',passwd=passwd)
 
         db = con.cursor()
-        print "You have successfully connected to mysql.\n"
+        print("You have successfully connected to mysql.\n")
 except:
-        print "You entered incorrect password.\n"
+        print("You entered incorrect password.\n")
         sys.exit(0)
 
 time0 = time.time()
@@ -55,7 +55,7 @@ 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
@@ -70,7 +70,7 @@ while line:
 	line2 = string.split(string.strip(line),'\t')
 	line2 = map(string.strip, line2)
 	if len(line2) != nfield:
-		print "Error : " + line
+		print(("Error : " + line))
 		isCont = 0
 
 	GeneList.append(line2[0])
@@ -78,7 +78,7 @@ while line:
 
 	kj+=1
 	if kj%100000 == 0:
-		print 'checked ',kj,' lines'
+		print(('checked ',kj,' lines'))
 
 GeneList = map(string.lower, GeneList)
 GeneList.sort()
@@ -87,14 +87,14 @@ 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)
@@ -109,20 +109,20 @@ 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
 #
 ########################################################################
-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()
@@ -146,7 +146,7 @@ Names = []
 for item in results:
 	Names.append(item[0])
 	
-print Names
+print(Names)
 
 Names = map(string.lower, Names)
 
@@ -170,7 +170,7 @@ while x<len(GeneList) and y<len(Names):
 		y += 1
 
 	if x%100000==0:
-		print 'check Name, checked %d lines'%x
+		print(('check Name, checked %d lines'%x))
 
 while x<len(GeneList):
 	GeneList2.append(GeneList[x])
@@ -180,20 +180,20 @@ 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"
+	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'
+print(('used ',time.time()-time0,' seconds'))
 #########################################################################
 #
 # Insert data into database
 #
 #########################################################################
-print 'getting ProbeSet/Id'
+print('getting ProbeSet/Id')
 
 
 #---- get Name/Id map ----#
@@ -202,16 +202,16 @@ 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'
+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
+print(("old_max = %d\n" % bmax))
 
 ##---- insert data ----##
 fp.seek(0)
@@ -255,8 +255,8 @@ 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()
 
diff --git a/scripts/maintenance/readProbeSetSE_v7.py b/scripts/maintenance/readProbeSetSE_v7.py
index 0b15ce09..79ed455f 100755
--- a/scripts/maintenance/readProbeSetSE_v7.py
+++ b/scripts/maintenance/readProbeSetSE_v7.py
@@ -82,14 +82,14 @@ while line:
     line2 = map(string.strip, line2)
     if len(line2) != nfield:
         isCont = 0
-        print("Error : " + line)
+        print(("Error : " + line))
 
     GeneList.append(line2[0])
     line = fp.readline()
 
     kj += 1
     if kj % 100000 == 0:
-        print('checked ', kj, ' lines')
+        print(('checked ', kj, ' lines'))
 
 GeneList = map(string.lower, GeneList)
 GeneList.sort()
@@ -98,7 +98,7 @@ 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
@@ -121,13 +121,13 @@ for item in header:
         Ids.append(db.fetchall()[0][0])
     except:
         isCont = 0
-        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'))
 
 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
@@ -178,7 +178,7 @@ while x < len(GeneList) and y < len(Names):
         y += 1
 
     if x % 100000 == 0:
-        print('check Name, checked %d lines' % x)
+        print(('check Name, checked %d lines' % x))
 
 while x < len(GeneList):
     GeneList2.append(GeneList[x])
@@ -190,12 +190,12 @@ for item in GeneList2:
     ferror.write(item + " doesn't exist \n")
     isCont = 0
 
-    print(item, " doesn't exist")
+    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
 ############################
@@ -244,9 +244,9 @@ while line:
 
         DataValues = []
         line = fp.readline()
-        print(CellId, " doesn't exist")
-        print('inserted ', kj, ' lines')
-        print('used ', time.time()-time0, ' seconds')
+        print((CellId, " doesn't exist"))
+        print(('inserted ', kj, ' lines'))
+        print(('used ', time.time()-time0, ' seconds'))
 
 if len(DataValues) > 0:
     DataValues = ','.join(DataValues)