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path: root/scripts/maintenance/readProbeSetMean_v7.py
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Diffstat (limited to 'scripts/maintenance/readProbeSetMean_v7.py')
-rwxr-xr-xscripts/maintenance/readProbeSetMean_v7.py292
1 files changed, 145 insertions, 147 deletions
diff --git a/scripts/maintenance/readProbeSetMean_v7.py b/scripts/maintenance/readProbeSetMean_v7.py
index e9c8f25c..43f084f4 100755
--- a/scripts/maintenance/readProbeSetMean_v7.py
+++ b/scripts/maintenance/readProbeSetMean_v7.py
@@ -9,19 +9,17 @@ import sys
import MySQLdb
import getpass
import time
-#import pdb
-#pdb.set_trace()
########################################################################
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
########################################################################
#
@@ -29,23 +27,25 @@ def translateAlias(str):
#
########################################################################
+
dataStart = 1
-GeneChipId = int( raw_input("Enter GeneChipId:") )
-ProbeSetFreezeId = int( raw_input("Enter ProbeSetFreezeId:") )
-input_file_name = raw_input("Enter file name with suffix:")
+GeneChipId = int(input("Enter GeneChipId:"))
+ProbeSetFreezeId = int(input("Enter ProbeSetFreezeId:"))
+input_file_name = 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()
@@ -55,163 +55,163 @@ 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 = map(string.strip, header)
+header = header.strip().split('\t')
+header = [x.strip() for x in 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 = line.strip().split('\t')
+ line2 = [x.strip() for x in line2]
+ if len(line2) != nfield:
+ print(("Error : " + line))
+ isCont = 0
- 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)
+GeneList = sorted(map(string.lower, GeneList))
+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 = map(string.strip, header)
-header = map(translateAlias, header)
+header = header.strip().split('\t')
+header = [x.strip() for x in header]
+header = list(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:
+ print((item, 'does not exist, check the if the strain name is correct'))
+ isCont = 0
-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 = map(string.strip, line2)
+line2 = line.strip().split('\t')
+line2 = [x.strip() for x in 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])
-
-print Names
+ Names.append(item[0])
-Names = map(string.lower, Names)
+print(Names)
-Names.sort() # -- Fixed the lower case problem of ProbeSets affx-mur_b2_at doesn't exist --#
+Names = sorted(map(string.lower, Names))
##---- 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, check if the ProbeSet name is correct"
- isCont = 0
-
-if isCont==0:
- sys.exit(0)
+ ferror.write(item + " doesn't exist \n")
+ 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 ----#
-db.execute('select %s, Id from ProbeSet where ChipId=%d order by %s' % (IdStr, GeneChipId, IdStr))
+db.execute('select %s, Id from ProbeSet where ChipId=%d order by %s' %
+ (IdStr, GeneChipId, IdStr))
results = db.fetchall()
NameIds = {}
for item in results:
- NameIds[item[0]] = item[1]
-print 'used ',time.time()-time0,' seconds'
+ NameIds[item[0]] = item[1]
+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)
@@ -222,53 +222,51 @@ kj = 0
values1 = []
values2 = []
while line:
- line2 = string.split(string.strip(line),'\t')
- line2 = map(string.strip, line2)
- PId = line2[0]
- recordId = NameIds[PId]
-
- maxDataId += 1
- datasorig = line2[dataStart:]
-
- ###### Data Table items ######
- i=0
- for item in datasorig:
- try:
- values1.append('(%d,%d,%s)' % (maxDataId, Ids[i], float(item)))
- except:
- pass
- i += 1
-
- values2.append("(%d,%d,%d)" % (ProbeSetFreezeId, recordId, maxDataId))
-
-
- ##---- insert into table ----##
- kj += 1
- if kj % 100 == 0:
- cmd = ','.join(values1)
- cmd = 'insert into ProbeSetData values %s' % cmd
- db.execute(cmd)
-
- cmd = ','.join(values2)
- cmd = 'insert into ProbeSetXRef(ProbeSetFreezeId, ProbeSetId, DataId) values %s' % cmd
- db.execute(cmd)
-
- values1=[]
- values2=[]
- print 'Inserted ', kj,' lines'
- print 'used ',time.time()-time0,' seconds'
-
- line = fp.readline()
-
-
-
-if len(values1)>0:
- cmd = ','.join(values1)
- cmd = 'insert into ProbeSetData values %s' % cmd
- db.execute(cmd)
-
- cmd = ','.join(values2)
- cmd = 'insert into ProbeSetXRef(ProbeSetFreezeId, ProbeSetId, DataId) values %s' % cmd
- db.execute(cmd)
+ line2 = line.strip().split('\t')
+ line2 = [x.strip() for x in line2]
+ PId = line2[0]
+ recordId = NameIds[PId]
+
+ maxDataId += 1
+ datasorig = line2[dataStart:]
+
+ ###### Data Table items ######
+ i = 0
+ for item in datasorig:
+ try:
+ values1.append('(%d,%d,%s)' % (maxDataId, Ids[i], float(item)))
+ except:
+ pass
+ i += 1
+
+ values2.append("(%d,%d,%d)" % (ProbeSetFreezeId, recordId, maxDataId))
+
+ ##---- insert into table ----##
+ kj += 1
+ if kj % 100 == 0:
+ cmd = ','.join(values1)
+ cmd = 'insert into ProbeSetData values %s' % cmd
+ db.execute(cmd)
+
+ cmd = ','.join(values2)
+ cmd = 'insert into ProbeSetXRef(ProbeSetFreezeId, ProbeSetId, DataId) values %s' % cmd
+ db.execute(cmd)
+
+ values1 = []
+ values2 = []
+ print(('Inserted ', kj, ' lines'))
+ print(('used ', time.time()-time0, ' seconds'))
+
+ line = fp.readline()
+
+
+if len(values1) > 0:
+ cmd = ','.join(values1)
+ cmd = 'insert into ProbeSetData values %s' % cmd
+ db.execute(cmd)
+
+ cmd = ','.join(values2)
+ cmd = 'insert into ProbeSetXRef(ProbeSetFreezeId, ProbeSetId, DataId) values %s' % cmd
+ db.execute(cmd)
con.close()
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 11:59:59 +0000