def test_index_finder2(self):
''' Test finding contiguous unequal bins '''
genomeBin = interactionMatrix.genomeBin((self.chrFile, 10, False))
self.assertEqual(genomeBin.findBinIndex('chr2', 0), 'nobin')
self.assertEqual(genomeBin.findBinIndex('chr2', 1), 5)
self.assertEqual(genomeBin.findBinIndex('chr2', 9), 5)
self.assertEqual(genomeBin.findBinIndex('chr2', 10), 6)
self.assertEqual(genomeBin.findBinIndex('chr2', 25), 7)
self.assertEqual(genomeBin.findBinIndex('chr2', 26), 8)
self.assertEqual(genomeBin.findBinIndex('chr2', 33), 8)
self.assertEqual(genomeBin.findBinIndex('chr2', 34), 'nobin')
def test_index_finder1(self):
''' Test finding non contiguous bins '''
genomeBin = interactionMatrix.genomeBin(self.inBed1)
self.assertEqual(genomeBin.findBinIndex('chr1', 10), 0)
self.assertEqual(genomeBin.findBinIndex('chr1', 9), 'nobin')
self.assertEqual(genomeBin.findBinIndex('chr1', 30), 1)
self.assertEqual(genomeBin.findBinIndex('chr1', 29), 'nobin')
self.assertEqual(genomeBin.findBinIndex('chr1', 20), 0)
self.assertEqual(genomeBin.findBinIndex('chr1', 21), 'nobin')
self.assertEqual(genomeBin.findBinIndex('chr1', 40), 1)
self.assertEqual(genomeBin.findBinIndex('chr1', 41), 'nobin')
self.assertEqual(genomeBin.findBinIndex('chr3', 10), 'nochr')
def test_matrix_generation(self):
''' Test creation of matrix '''
genomeBin = interactionMatrix.genomeBin((self.chrFile, 10, True))
countMatrix, logArray = genomeBin.generateMatrix(self.inFrag,
threads=4)
self.assertTrue(
np.array_equal(
countMatrix,
np.array([[2, 0, 0, 0, 0, 0, 1], [0, 0, 0, 1, 0, 0, 0],
[0, 0, 0, 0, 2, 0, 0], [0, 1, 0, 0, 0, 0, 0],
[0, 0, 2, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0],
[1, 0, 0, 0, 0, 0, 0]])))
self.assertTrue(np.array_equal(logArray, np.array([10, 2, 3, 5])))
def test_bin_generation3(self):
''' Test unequal bin creation with large bins '''
genomeBin = interactionMatrix.genomeBin((self.chrFile, 40, False))
self.assertTrue(
all(genomeBin.binDict['chr1']['start'] == np.array(
[1, 24], dtype=np.uint32)))
self.assertTrue(
all(genomeBin.binDict['chr1']['end'] == np.array([23, 46],
dtype=np.uint32)))
self.assertTrue(
all(genomeBin.binDict['chr1']['index'] == np.array(
[0, 1], dtype=np.uint32)))
self.assertTrue(
all(genomeBin.binDict['chr2']['start'] == np.array(
[1], dtype=np.uint32)))
self.assertTrue(
all(genomeBin.binDict['chr2']['end'] == np.array([33],
dtype=np.uint32)))
self.assertTrue(
all(genomeBin.binDict['chr2']['index'] == np.array(
[2], dtype=np.uint32)))
def test_bin_generation2(self):
''' Test unequal bin creation with small bins '''
genomeBin = interactionMatrix.genomeBin((self.chrFile, 11, False))
self.assertTrue(
all(genomeBin.binDict['chr1']['start'] == np.array(
[1, 11, 20, 29, 38], dtype=np.uint32)))
self.assertTrue(
all(genomeBin.binDict['chr1']['end'] == np.array(
[10, 19, 28, 37, 46], dtype=np.uint32)))
self.assertTrue(
all(genomeBin.binDict['chr1']['index'] == np.array(
[0, 1, 2, 3, 4], dtype=np.uint32)))
self.assertTrue(
all(genomeBin.binDict['chr2']['start'] == np.array(
[1, 12, 23], dtype=np.uint32)))
self.assertTrue(
all(genomeBin.binDict['chr2']['end'] == np.array([11, 22, 33],
dtype=np.uint32)))
self.assertTrue(
all(genomeBin.binDict['chr2']['index'] == np.array(
[5, 6, 7], dtype=np.uint32)))
def test_bin_generation7(self):
''' Test bin creation from bed file '''
genomeBin = interactionMatrix.genomeBin(self.inBed1)
self.assertTrue(
all(genomeBin.binDict['chr1']['start'] == np.array(
[10, 30], dtype=np.uint32)))
self.assertTrue(
all(genomeBin.binDict['chr1']['end'] == np.array([20, 40],
dtype=np.uint32)))
self.assertTrue(
all(genomeBin.binDict['chr1']['index'] == np.array(
[0, 1], dtype=np.uint32)))
self.assertTrue(
all(genomeBin.binDict['chr2']['start'] == np.array(
[5], dtype=np.uint32)))
self.assertTrue(
all(genomeBin.binDict['chr2']['end'] == np.array([15],
dtype=np.uint32)))
self.assertTrue(
all(genomeBin.binDict['chr2']['index'] == np.array(
[2], dtype=np.uint32)))
def test_bin_generation6(self):
''' Test unequal bin creation with small bins '''
genomeBin = interactionMatrix.genomeBin((self.chrFile, 41, True))
self.assertTrue(
all(genomeBin.binDict['chr1']['start'] == np.array(
[3], dtype=np.uint32)))
self.assertTrue(
all(genomeBin.binDict['chr1']['end'] == np.array([43],
dtype=np.uint32)))
self.assertTrue(
all(genomeBin.binDict['chr1']['index'] == np.array(
[0], dtype=np.uint32)))
self.assertTrue(
all(genomeBin.binDict['chr2']['start'] == np.array(
[], dtype=np.uint32)))
self.assertTrue(
all(genomeBin.binDict['chr2']['end'] == np.array([],
dtype=np.uint32)))
self.assertTrue(
all(genomeBin.binDict['chr2']['index'] == np.array(
[], dtype=np.uint32)))
def test_bin_generation6(self):
''' Test unequal bin creation with small bins '''
genomeBin = interactionMatrix.genomeBin((self.chrFile, 41, True))
self.assertTrue(
all(genomeBin.binDict['chr1']['start'] == np.array(
[2, 13, 24, 35], dtype=np.uint32)))
self.assertTrue(
all(genomeBin.binDict['chr1']['end'] == np.array([12, 23, 34, 45],
dtype=np.uint32)))
self.assertTrue(
all(genomeBin.binDict['chr1']['index'] == np.array(
[0, 1, 2, 3], dtype=np.uint32)))
self.assertTrue(
all(genomeBin.binDict['chr2']['start'] == np.array(
[1, 12, 23], dtype=np.uint32)))
self.assertTrue(
all(genomeBin.binDict['chr2']['end'] == np.array([11, 22, 33],
dtype=np.uint32)))
self.assertTrue(
all(genomeBin.binDict['chr2']['index'] == np.array(
[4, 5, 6], dtype=np.uint32)))
elif args.chrSize and args.binSize:
binData = (args.chrSize, args.binSize, args.equal)
print 'Parameters:\n\t%s\n\t%s\n\t%s' %(
'max bin size: %s' %(args.binSize),
'bin size equal: %s' %(args.equal),
'minimum bin count: %s' %(args.minCount)
)
else:
raise IOError('bed file or chromosome file and bin size must be provided')
# Create output files
args.bedFile = args.outPrefix + '.bed'
args.biasFile = args.outPrefix + '.bias'
args.countMatrix = args.outPrefix + '.countMatrix'
args.normMatrix = args.outPrefix + '.normMatrix'
# Create bin object and save bed
genomeBins = interactionMatrix.genomeBin(binData)
genomeBins.writeBed(args.bedFile)
# Count interactions
countMatrix, logArray = interactionMatrix.generateMatrix(
args.inFile, genomeBins, args.threads
)
# Save interactions
np.savetxt(args.countMatrix, countMatrix, '%s', '\t',
header = '\t'.join(genomeBins.binNames), comments = '')
# Print Interaction Data
print '\nInteraction Data\n\t%s\n\t%s\n\t%s\n\t%s' %(
'total: %s' %(logArray[0]),
'accepted: %s' %(logArray[3]),
'no chromosome: %s' %(logArray[1]),
'no bin: %s' %(logArray[2])
)
'minimum bin count: %s' %
(args.minCount))
elif args.chrSize and args.binSize:
binData = (args.chrSize, args.binSize, args.equal)
print 'Parameters:\n\t%s\n\t%s\n\t%s' % (
'max bin size: %s' % (args.binSize), 'bin size equal: %s' %
(args.equal), 'minimum bin count: %s' % (args.minCount))
else:
raise IOError('bed file or chromosome file and bin size must be provided')
# Create output files
args.bedFile = args.outPrefix + '.bed'
args.biasFile = args.outPrefix + '.bias'
args.countMatrix = args.outPrefix + '.countMatrix'
args.normMatrix = args.outPrefix + '.normMatrix'
# Create bin object and save bed
genomeBins = interactionMatrix.genomeBin(binData)
genomeBins.writeBed(args.bedFile)
# Count interactions
countMatrix, logArray = interactionMatrix.generateMatrix(
args.inFile, genomeBins, args.threads)
# Save interactions
np.savetxt(args.countMatrix,
countMatrix,
'%s',
'\t',
header='\t'.join(genomeBins.binNames),
comments='')
# Print Interaction Data
print '\nInteraction Data\n\t%s\n\t%s\n\t%s\n\t%s' % (
'total: %s' % (logArray[0]), 'accepted: %s' %
(logArray[3]), 'no chromosome: %s' % (logArray[1]), 'no bin: %s' %
def test_index_finder3(self):
''' Test finding contiguous equal bins '''
genomeBin = interactionMatrix.genomeBin((self.chrFile, 10, True))
self.assertEqual(genomeBin.findBinIndex('chr1', 1), 'nobin')
self.assertEqual(genomeBin.findBinIndex('chr2', 32), 'nobin')
self.assertEqual(genomeBin.findBinIndex('chr2', 31), 6)
def test_bin_generation8(self):
''' Test overlapping bins in bed file '''
with self.assertRaises(IOError):
interactionMatrix.genomeBin(self.inBed2)