Replace DOS style line endings with UNIX style ones

* scripts/maintenance/readProbeSetSE_v7.py: Run *dos2unix* against file

1 files changed, 256 insertions, 256 deletions

diff --git a/scripts/maintenance/readProbeSetSE_v7.py b/scripts/maintenance/readProbeSetSE_v7.py
index 2a1d44ff..0b15ce09 100755
--- a/scripts/maintenance/readProbeSetSE_v7.py
+++ b/scripts/maintenance/readProbeSetSE_v7.py
@@ -1,256 +1,256 @@
-#!/usr/bin/python2

-"""This script use the nearest marker to the transcript as control, increasing permutation rounds according to the p-value"""

-########################################################################

-# Last Updated Sep 27, 2011 by Xiaodong

-# This version fix the bug that incorrectly exclude the first 2 probesetIDs

-########################################################################

-

-import string

-import sys

-import MySQLdb

-import getpass

-import time

-

-

-def translateAlias(str):

-    if str == "B6":

-        return "C57BL/6J"

-    elif str == "D2":

-        return "DBA/2J"

-    else:

-        return str

-

-########################################################################

-#

-#  Indicate Data Start Position, ProbeFreezeId, GeneChipId, DataFile

-#

-########################################################################

-

-

-dataStart = 1

-

-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)

-

-    db = con.cursor()

-    print("You have successfully connected to mysql.\n")

-except:

-    print("You entered incorrect password.\n")

-    sys.exit(0)

-

-time0 = time.time()

-########################################################################

-#

-#  Indicate Data Start Position, ProbeFreezeId, GeneChipId, DataFile

-#

-########################################################################

-

-#GeneChipId = 4

-#dataStart = 1

-# ProbeSetFreezeId = 359 #JAX Liver 6C Affy M430 2.0 (Jul11) MDP

-#fp = open("GSE10493_AllSamples_6C_Z_AvgSE.txt", 'rb')

-

-

-#########################################################################

-#

-#  Check if each line have same number of members

-#  generate the gene list of expression data here

-#

-#########################################################################

-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)

-nfield = len(header)

-line = fp.readline()

-

-kj = 0

-while line:

-    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()

-

-    kj += 1

-    if kj % 100000 == 0:

-        print('checked ', kj, ' lines')

-

-GeneList = map(string.lower, GeneList)

-GeneList.sort()

-

-if isCont == 0:

-    sys.exit(0)

-

-

-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')

-

-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[dataStart:]

-Ids = []

-for item in header:

-    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)

-

-

-print('used ', time.time()-time0, ' seconds')

-########################################################################

-#

-# 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)

-PId = line2[0]

-

-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'

-

-

-##---- get Name/TargetId list from database ----##

-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 --#

-

-##---- 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

-ferror = open("ProbeSetError.txt", "wb")

-for item in GeneList2:

-    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')

-#############################

-# 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))

-results = db.fetchall()

-

-ProbeNameId = {}

-for Name, Id in results:

-    ProbeNameId[Name] = Id

-

-ferror = open("ProbeError.txt", "wb")

-

-DataValues = []

-

-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")

-    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()

+#!/usr/bin/python2
+"""This script use the nearest marker to the transcript as control, increasing permutation rounds according to the p-value"""
+########################################################################
+# Last Updated Sep 27, 2011 by Xiaodong
+# This version fix the bug that incorrectly exclude the first 2 probesetIDs
+########################################################################
+
+import string
+import sys
+import MySQLdb
+import getpass
+import time
+
+
+def translateAlias(str):
+    if str == "B6":
+        return "C57BL/6J"
+    elif str == "D2":
+        return "DBA/2J"
+    else:
+        return str
+
+########################################################################
+#
+#  Indicate Data Start Position, ProbeFreezeId, GeneChipId, DataFile
+#
+########################################################################
+
+
+dataStart = 1
+
+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)
+
+    db = con.cursor()
+    print("You have successfully connected to mysql.\n")
+except:
+    print("You entered incorrect password.\n")
+    sys.exit(0)
+
+time0 = time.time()
+########################################################################
+#
+#  Indicate Data Start Position, ProbeFreezeId, GeneChipId, DataFile
+#
+########################################################################
+
+#GeneChipId = 4
+#dataStart = 1
+# ProbeSetFreezeId = 359 #JAX Liver 6C Affy M430 2.0 (Jul11) MDP
+#fp = open("GSE10493_AllSamples_6C_Z_AvgSE.txt", 'rb')
+
+
+#########################################################################
+#
+#  Check if each line have same number of members
+#  generate the gene list of expression data here
+#
+#########################################################################
+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)
+nfield = len(header)
+line = fp.readline()
+
+kj = 0
+while line:
+    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()
+
+    kj += 1
+    if kj % 100000 == 0:
+        print('checked ', kj, ' lines')
+
+GeneList = map(string.lower, GeneList)
+GeneList.sort()
+
+if isCont == 0:
+    sys.exit(0)
+
+
+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')
+
+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[dataStart:]
+Ids = []
+for item in header:
+    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)
+
+
+print('used ', time.time()-time0, ' seconds')
+########################################################################
+#
+# 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)
+PId = line2[0]
+
+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'
+
+
+##---- get Name/TargetId list from database ----##
+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 --#
+
+##---- 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
+ferror = open("ProbeSetError.txt", "wb")
+for item in GeneList2:
+    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')
+#############################
+# 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))
+results = db.fetchall()
+
+ProbeNameId = {}
+for Name, Id in results:
+    ProbeNameId[Name] = Id
+
+ferror = open("ProbeError.txt", "wb")
+
+DataValues = []
+
+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")
+    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()