def testBin(self):
# first do all liquidation together at once, then do it in two runs appending, and verify everything matches
bin_size = len(self.sequence1)
together_dir_path = os.path.join(self.dir_path, 'together')
liquidator = blb.BinLiquidator(bin_size=bin_size,
output_directory=together_dir_path,
bam_file_path=self.dir_path)
appending_dir = os.path.join(self.dir_path, 'appending')
#print 'liquidating bams at path:', self.bam1_file_path
liquidator = blb.BinLiquidator(bin_size=bin_size,
output_directory=appending_dir,
bam_file_path=self.bam1_file_path)
appending_h5_path = os.path.join(appending_dir, 'counts.h5')
liquidator = blb.BinLiquidator(bin_size=bin_size,
output_directory=os.path.join(
self.dir_path,
'appending_extra_without_h5_file'),
bam_file_path=self.bam2_file_path,
counts_file_path=appending_h5_path)
with tables.open_file(os.path.join(together_dir_path,
'counts.h5')) as together_h5:
with tables.open_file(appending_h5_path) as appending_h5:
self.assertEqual(str(together_h5.root.bin_counts[:]),
str(appending_h5.root.bin_counts[:]))
self.assertEqual(str(together_h5.root.normalized_counts[:]),
str(appending_h5.root.normalized_counts[:]))
self.assertEqual(str(together_h5.root.summary[:]),
str(appending_h5.root.summary[:]))
self.assertEqual(str(together_h5.root.sorted_summary[:]),
str(appending_h5.root.sorted_summary[:]))
def test_bin_liquidation(self):
bin_size = len(self.sequence)
liquidator = blb.BinLiquidator(bin_size=bin_size,
output_directory=os.path.join(
self.dir_path, 'output'),
bam_file_path=self.bam_file_path)
liquidator.flatten()
with tables.open_file(liquidator.counts_file_path) as counts:
self.assertEqual(1, len(
counts.root.files)) # 1 since only a single bam file
file_record = counts.root.files[0]
self.assertEqual(
1, file_record['length']) # 1 since only a single read
self.assertEqual(1, file_record['key'])
self.assertEqual(1, len(counts.root.bin_counts)
) # 1 since 1 bin accommodates full sequence
record = counts.root.bin_counts[0]
self.assertEqual(0, record['bin_number'])
self.assertEqual(self.chromosome, record['chromosome'].decode())
self.assertEqual(
len(self.sequence),
record['count']) # count represents how many base pair reads
def test_liquidation_in_long_directory(self):
self.dir_path = tempfile.mkdtemp(prefix='blt_' + 'a' * 16)
truncated_cell_type = os.path.basename(self.dir_path)[:15]
self.bam_file_path = create_bam(self.dir_path, [self.chromosome],
self.sequence)
bin_size = len(self.sequence)
liquidator = blb.BinLiquidator(bin_size=bin_size,
output_directory=os.path.join(
self.dir_path, 'output'),
bam_file_path=self.bam_file_path)
with tables.open_file(liquidator.counts_file_path) as counts:
self.assertEqual(1, len(
counts.root.files)) # 1 since only a single bam file
file_record = counts.root.files[0]
self.assertEqual(
1, file_record['length']) # 1 since only a single read
self.assertEqual(1, file_record['key'])
self.assertEqual(1, len(counts.root.bin_counts)
) # 1 since 1 bin accommodates full sequence
record = counts.root.bin_counts[0]
self.assertEqual(0, record['bin_number'])
self.assertEqual(truncated_cell_type, record['cell_type'].decode())
self.assertEqual(self.chromosome, record['chromosome'].decode())
self.assertEqual(
len(self.sequence),
record['count']) # count represents how many base pair reads
def testOverridingBlackList(self):
chromosomes = ['chr1', 'chr2', 'chr2_random']
sequence = 'ATTTAAAAATTAATTTAATGCTTGGCTAAATCTTAATTACATATATAATT'
bam_file_path = create_bam(self.dir_path,
chromosomes,
sequence,
file_name='multiple.bam')
bin_size = len(sequence)
liquidator = blb.BinLiquidator(bin_size=bin_size,
output_directory=os.path.join(
self.dir_path, 'output'),
bam_file_path=bam_file_path,
blacklist=[])
with tables.open_file(liquidator.counts_file_path) as counts:
self.assertEqual(1, len(
counts.root.files)) # 1 since only a single bam file
file_record = counts.root.files[0]
self.assertEqual(
3, file_record['length']) # 1 read for each chromosome
self.assertEqual(1, file_record['key'])
self.assertEqual(
3, len(counts.root.bin_counts
)) # 1 for each chromosome that should be liquidated
for record_index, chromosome in enumerate(chromosomes):
record = counts.root.bin_counts[record_index]
self.assertEqual(0, record['bin_number'])
self.assertEqual(chromosome, record['chromosome'].decode())
self.assertEqual(len(sequence), record['count']
) # count represents how many base pair reads
def test_bin_liquidation_zero_bin_size(self):
with self.assertRaises(Exception):
liquidator = blb.BinLiquidator(bin_size=0,
output_directory=os.path.join(
self.dir_path, 'output'),
bam_file_path=self.bam_file_path)
liquidator.batch(extension=0, sense='.')
def test_bin_long_bam_file_name(self):
long_file_name = 'x' * 65 # more than Float64Col
long_file_path = os.path.join(self.dir_path, long_file_name)
shutil.copyfile(self.bam_file_path, long_file_path)
shutil.copyfile(self.bam_file_path + '.bai', long_file_path + '.bai')
bin_liquidator = blb.BinLiquidator(bin_size=len(self.sequence),
output_directory=os.path.join(
self.dir_path, 'bin_output'),
bam_file_path=long_file_path)