# Print output header for the <A_file>
output_header(args, fileA)
# Foreach <B_files>
if args['-c']: FH = open('testFiles/summary', 'w')
mnRandom = 0
for fileB_name in args['<B_files>']:
# Create a Dataset object based on the <B_file>
fileB = Dataset(fileB_name)
fileB.calcDataCoords(refGenome)
if args['-v'] in ['all', 'fileB']: fileB.printDataset('fileB')
# Compare <A_file> and <B_file>
matrix = fileA.compareData(fileB, args)
matrix.addGenomeSize(refGenome.getSize()[1])
randMatrices = []
# Foreach M number of randomizations
for mRandom in range(int(args['-m'])):
# Create a randomization of the <A_file>
randFileA = fileA.randomize(refGenome, args,
'randGenomeA_%d' % mRandom)
if args['-v'] in ['all', 'remap']:
randFileA.printDataset('randFileA_%d' % mRandom)
# Foreach N number of randomizations
for nRandom in range(int(args['-n'])):
# Create a randomization of the <B_file>
# Print output header for the <A_file>
output_header(args, args['<A_file>'])
# Foreach <B_files>
if args['-c']: FH = open('testFiles/summary', 'w')
mnRandom = 0
for fileB_name in args['<B_files>']:
# Create a Dataset object based on the <B_file>
fileB = Dataset(fileB_name)
fileB.calcDataCoords(refGenome)
if args['-v'] in ['all', 'fileB']: fileB.printDataset('fileB')
# Compare <A_file> and <B_file>
matrix = fileA.compareData(fileB, args)
matrix.addGenomeSize(refGenome.getSize()[1])
randMatrices = []
# Foreach M number of randomizations
for mRandom in range(int(args['-m'])):
# Create a randomization of the <A_file>
randFileA = fileA.randomize(refGenome, args,
'randGenomeA_%d' % mRandom)
if args['-v'] in ['all', 'remap']:
randFileA.printDataset('randFileA_%d' % mRandom)
# Foreach N number of randomizations
for nRandom in range(int(args['-n'])):
# Create a randomization of the <B_file>
