From 5c5aefc79d45d66ab30bdbbc5dab24b3f5f79dc2 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Mon, 17 Aug 2020 20:35:53 +0300 Subject: Apply pep8 * scripts/maintenance/readProbeSetSE_v7.py: Apply pep8 to file to replace tabs with spaces and use correct indentation. --- scripts/maintenance/readProbeSetSE_v7.py | 258 ++++++++++++++++--------------- 1 file changed, 130 insertions(+), 128 deletions(-) (limited to 'scripts') 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 xNames[y]: - y += 1 - - if x%100000==0: - print 'check Name, checked %d lines'%x - -while 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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