def test_index_finder2(self):
''' Test finding contiguos 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_bin_generation6(self):
''' Test unequal bin creation with small bins '''
genomeBin = interactionMatrix.genomeBin((self.chrFile,41,True))
chr1DF = pd.DataFrame()
chr1DF['chr'] = np.array(['chr1'])
chr1DF['start'] = np.array([3])
chr1DF['end'] = np.array([43])
chr1DF['index'] = np.array([0])
chr2DF = pd.DataFrame(columns = ['chr','start','end','index'])
self.assertTrue(all(genomeBin.binDict['chr1'] == chr1DF))
self.assertTrue(all(genomeBin.binDict['chr2'] == chr2DF))
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_bin_generation4(self):
''' Test equal bin creation with small bins '''
genomeBin = interactionMatrix.genomeBin((self.chrFile,10,True))
chr1DF = pd.DataFrame()
chr1DF['chr'] = np.array(['chr1'] * 4)
chr1DF['start'] = np.array([4,14,24,34])
chr1DF['end'] = np.array([13,23,33,43])
chr1DF['index'] = np.array([0,1,2,3])
chr2DF = pd.DataFrame()
chr2DF['chr'] = np.array(['chr2'] * 3)
chr2DF['start'] = np.array([2,12,22])
chr2DF['end'] = np.array([11,21,31])
chr2DF['index'] = np.array([4,5,6])
self.assertTrue(all(genomeBin.binDict['chr1'] == chr1DF))
self.assertTrue(all(genomeBin.binDict['chr2'] == chr2DF))
def test_bin_generation3(self):
''' Test unequal bin creation with large bins '''
genomeBin = interactionMatrix.genomeBin((self.chrFile,40,False))
chr1DF = pd.DataFrame()
chr1DF['chr'] = np.array(['chr1'] * 2)
chr1DF['start'] = np.array([1,24])
chr1DF['end'] = np.array([23,46])
chr1DF['index'] = np.array([0,1])
chr2DF = pd.DataFrame()
chr2DF['chr'] = np.array(['chr2'])
chr2DF['start'] = np.array([1])
chr2DF['end'] = np.array([33])
chr2DF['index'] = np.array([2])
self.assertTrue(all(genomeBin.binDict['chr1'] == chr1DF))
self.assertTrue(all(genomeBin.binDict['chr2'] == chr2DF))
def test_bin_generation2(self):
''' Test unequal bin creation with small bins '''
genomeBin = interactionMatrix.genomeBin((self.chrFile,11,False))
chr1DF = pd.DataFrame()
chr1DF['chr'] = np.array(['chr1'] * 5)
chr1DF['start'] = np.array([1,11,20,29,38])
chr1DF['end'] = np.array([10,19,28,37,46])
chr1DF['index'] = np.array([0,1,2,3,4])
chr2DF = pd.DataFrame()
chr2DF['chr'] = np.array(['chr2'] * 3)
chr2DF['start'] = np.array([1,12,23])
chr2DF['end'] = np.array([11,22,33])
chr2DF['index'] = np.array([5,6,7])
self.assertTrue(all(genomeBin.binDict['chr1'] == chr1DF))
self.assertTrue(all(genomeBin.binDict['chr2'] == chr2DF))
def test_bin_generation7(self):
''' Test bin creation from bed file '''
genomeBin = interactionMatrix.genomeBin(self.inBed1)
chr1DF = pd.DataFrame()
chr1DF['chr'] = np.array(['chr1'] * 2)
chr1DF['start'] = np.array([10,30])
chr1DF['end'] = np.array([20,40])
chr1DF['index'] = np.array([0,1])
chr2DF = pd.DataFrame()
chr2DF['chr'] = np.array(['chr2'])
chr2DF['start'] = np.array([5])
chr2DF['end'] = np.array([15])
chr2DF['index'] = np.array([2])
self.assertTrue(all(genomeBin.binDict['chr1'] == chr1DF))
self.assertTrue(all(genomeBin.binDict['chr2'] == chr2DF))
def test_matrix_generation(self):
''' Test creation of matrix '''
genomeBin = interactionMatrix.genomeBin((self.chrFile,10,True))
countMatrix, logArray = interactionMatrix.generateMatrix(
self.inFrag, genomeBin, 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])))
# Extract and print parameters to create bins
if args['bed']:
binData = args['<bedfile>']
print 'Parameters:\n\t%s\n\t%s' %(
'bed file provided',
'minimum bin count: %s' %(args['<mincount>'])
)
else:
binData = (args['<chrfile>'], args['<binsize>'], args['--equal'])
print 'Parameters:\n %s\n %s\n %s' %(
'max bin size: %s' %(args['<binsize>']),
'bin size equal: %s' %(args['--equal']),
'minimum bin count: %s' %(args['<mincount>'])
)
# Create bin object and save bed
genomeBins = interactionMatrix.genomeBin(binData)
# Sequentially process input files
failedBins = np.full(genomeBins.binCount, False, dtype=bool)
matrixFileList = []
for f in args['<inputfiles>']:
# Extract sample names
sampleName = re.search('([^/]*)\.fragLigations.gz$',f).group(1)
# Create output file prefix
if args['--label']:
outPrefix = args['<outdir>'] + sampleName + '_' + args['--label']
else:
outPrefix = args['<outdir>'] + sampleName
# Create output file names
bedFile = outPrefix + '.bed'
matrixFile = outPrefix + '.countMatrix.gz'
biasFile = outPrefix + '.bias'
def test_bin_generation8(self):
''' Test overlapping bins in bed file '''
with self.assertRaises(IOError):
interactionMatrix.genomeBin(self.inBed2)