diff options
Diffstat (limited to 'scripts/maintenance/readProbeSetMean_v7.py')
| -rwxr-xr-x | scripts/maintenance/readProbeSetMean_v7.py | 40 |
1 files changed, 20 insertions, 20 deletions
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() |