def test_async_mappable_regions_50_hisat(tests_config, chrom, hisat2):
filename = os.path.join('sgains/tests/data',
"{}.50mer.mappable.regions.txt.gz".format(chrom))
gold_df = pd.read_csv(filename,
sep='\t',
compression='gzip',
header=None,
names=['chrom', 'start', 'end'])
with io.StringIO() as outfile:
pipeline = MappableRegionsPipeline(tests_config, hisat2)
pipeline.generate_mappable_regions([chrom], 50, outfile=outfile)
outfile.flush()
infile = io.StringIO(outfile.getvalue())
df = pd.read_csv(infile,
sep='\t',
header=None,
names=['chrom', 'start', 'end'])
print(df.head())
assert np.all(df.columns == gold_df.columns)
assert len(df) == len(gold_df)
assert np.all(df.start == gold_df.start)
assert np.all(df.end == gold_df.end)
def test_generate_mappable_regions_hisat(tests_config, hisat2):
assert hisat2 is not None
pipeline = MappableRegionsPipeline(tests_config, hisat2)
pipeline.generate_mappable_regions(['chrM'], 100)
def test_generate_mappable_regions_bwa(tests_config, bwa):
assert bwa is not None
pipeline = MappableRegionsPipeline(tests_config, bwa)
pipeline.generate_mappable_regions(['chrM'], 100)
def test_generate_mappable_regions(tests_config):
pipeline = MappableRegionsPipeline(tests_config)
pipeline.generate_mappable_regions(['chrM'], 100)