with open(options.symbolmap, 'r') as fin:
symbolMap = pickle.load(fin)
seqMap = DataFile.generateSeqMap(progDict, symbolMap, paramsDict)
if hasattr(options, 'number'):
minNumScans = int(options.number)
else:
minNumScans = 1
processedInfo = {}
if options.lads:
LADSdict = eval(options.lads)
for tdvfile in LADSdict.keys():
LADSScanInfo = DataFile.getScanInfo(tdvfile, dbDict['LADS']['fields'], delimiter='\t')
processedInfo[LADSdict[tdvfile]] = An.preprocessLADSScanInfo(LADSScanInfo, seqMap[LADSdict[tdvfile]], paramsDict['LADS Parameters']['pair configurations'], dbDict['LADS']['fieldmap'])
if options.mascot:
MASCOTdict = eval(options.mascot)
processedInfo.update(parseDBScans(MASCOTdict, 'MASCOT', seqMap, dbDict))
if options.sequest:
SEQUESTdict = eval(options.sequest)
processedInfo.update(parseDBScans(SEQUESTdict, 'SEQUEST', seqMap, dbDict))
cols = ['ScanF']
progNames = processedInfo.keys()
cols.extend([val for val in dbDict[progDict[progNames[0]]]['cols']])
outFile = open(options.output, 'w')
outFile.write(','.join([col for col in cols]) + '\n')
