def test_read_write(self):
zip_path = './data/test.bgzf'
with BlockZip(zip_path, 'w') as f:
f.write('chr1', 100, False, 'yes')
f.write('chr1', 101, False, 'yes')
f.write('chr2', 2101, True, 'yes')
f.write('chrX', 0, False, 'X')
with BlockZip(zip_path, 'r') as f:
self.assertEqual(f[('chr1', 100, False)], 'yes')
self.assertEqual(f[('chr1', 0, False)], None)
self.assertEqual(f[('chrX', 0, False)], 'X')
self.assertEqual(f[('chr2', 2101, True)], 'yes')
self.assertEqual(f[('chr1', 0, True)], None)
# Test verification:
with BlockZip(zip_path, 'r') as f:
f.verify()
with BlockZip(zip_path, 'w') as f:
f.write('chr1', 101, False, 'yes')
f.write('chr1', 100, False, 'yes')
f.write('chr2', 2101, True, 'yes')
f.write('chrX', 0, False, 'X')
with BlockZip(zip_path, 'r') as bz:
self.assertRaises(ValueError, bz.verify)
# Test for missing index:
os.remove(zip_path + '.idx')
self.assertRaises(ValueError, BlockZip, './non_existing.bgzf', 'r')
os.remove(zip_path)
self.assertRaises(ValueError, BlockZip, './non_existing.bgzf', 'r')
def __init__(self,
mapability_safe_file_path,
read_all=False,
dont_open=True):
self.args = locals().copy()
del self.args['self']
self.mapability_safe_file_path = mapability_safe_file_path
if not dont_open:
self.handle = BlockZip(mapability_safe_file_path, 'r')
def site_is_mapable(self, contig, ds, strand):
if self.handle is None:
self.handle = BlockZip(self.mapability_safe_file_path, 'r')
""" Obtain if a restriction site is mapable or not
Args:
contig (str) : contig of site to look up
ds (int) : zero based coordinate of site to look up
strand (bool) : strand of site to look up (False: FWD, True: REV)
Returns:
site_is_mapable (bool) : True when the site is uniquely mapable, False otherwise
"""
if self.handle[contig, ds, strand] == 'ok':
return True
return False
if read_site == site_pos and site_chrom == read_contig and read.is_reverse == strand: # Correct assignment
sites[key]['correct'] += 1
else:
# Assign a missing count to the origin site:
sites[key]['lost'] += 1
# Assing a wrong annotation to the target site:
if key_mapped not in sites:
sites[key_mapped] = {'correct': 0, 'wrong_gain': 0, 'lost': 0}
sites[key_mapped]['wrong_gain'] += 1
print("Writing site statistics ...")
outtab = f'simulated_{args.digest_sequence}_single_{r1_read_length}.mappability.stats.bgzf'
outtabsafe = f'simulated_{args.digest_sequence}_single_{r1_read_length}.mappability.safe.bgzf'
keys = sorted([(contig, pos, strand)
for (contig, pos, strand) in sites.keys()
if contig is not None])
with BlockZip(outtab, 'w') as stats, BlockZip(outtabsafe, 'w') as safe:
for (contig, pos, strand) in keys:
measured = sites[(contig, pos, strand)]
stats.write(
contig, pos, strand,
f'{measured["correct"]}\t{measured["lost"]}\t{measured["wrong_gain"]}'
)
if measured['wrong_gain'] == 0 and measured[
'lost'] == 0 and measured['correct'] == 1:
safe.write(contig, pos, strand, 'ok')
def __getitem__(self, contig_ds_strand):
if self.handle is None:
self.handle = BlockZip(self.mapability_safe_file_path, 'r')
contig, ds, strand = contig_ds_strand
return self.handle[contig, ds, strand]
def __init__(self, mapability_safe_file_path):
self.mapability_safe_file_path = mapability_safe_file_path
self.handle = BlockZip(mapability_safe_file_path, 'r')