diff options
| -rwxr-xr-x | scripts/maintenance/readProbeSetSE_v7.py | 258 |
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()
-
-
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