async def test_bowtie_mappings(tests_config, event_loop, chrom):
event_loop.set_debug(True)
pipeline = MappableRegionsPipeline(tests_config)
bowtie = await pipeline.async_start_bowtie()
reads_generator = pipeline.generate_reads([chrom], 100)
writer = asyncio.Task(
pipeline.async_write_reads_generator(bowtie.stdin, reads_generator))
infile = bowtie.stdout
while True:
line = await infile.readline()
if not line:
break
line = line.decode()
if line[0] == '@':
# comment
continue
mapping = Mapping.parse_sam(line)
if mapping.flag == 0:
# print(mapping)
chromosome, pos = mapping.name.split('.')
assert int(pos) == mapping.start
assert chrom == chromosome
await writer
async def test_generate_reads(tests_config):
pipeline = MappableRegionsPipeline(tests_config)
generator = pipeline.generate_reads(['chr1'], 100)
for num, rec in enumerate(generator):
print(rec.id, len(rec))
if num >= 10:
break
generator.close()
def test_reads_generator(tests_config):
pipeline = MappableRegionsPipeline(tests_config)
reads_generator = pipeline.generate_reads(['chrM'], 100)
# ouptut_writer = pipeline.mappable_regions_writer()
count = 0
for _read in reads_generator:
# print(read)
count += 1
print(count)
assert 16472 == count
async def test_async_mappings_generator(tests_config, event_loop):
# Enable debugging
event_loop.set_debug(True)
pipeline = MappableRegionsPipeline(tests_config)
bowtie = await pipeline.async_start_bowtie()
reads_generator = pipeline.generate_reads(['chrM'], 100)
writer = asyncio.Task(
pipeline.async_write_reads_generator(bowtie.stdin, reads_generator))
async for mapping in pipeline.async_mappable_regions_generator(
bowtie.stdout):
print(mapping)
await bowtie.wait()
await writer