# third-party
import Bio.SeqIO
import pytest
# intra-project
import util.file
from util.misc import available_cpu_count
from tools.samtools import SamtoolsTool
logging.getLogger('botocore').setLevel(logging.WARNING)
logging.getLogger('boto3').setLevel(logging.WARNING)
if 'PYTEST_XDIST_WORKER_COUNT' in os.environ:
_CPUS = 1
else:
_CPUS = available_cpu_count()
def make_slow_test_marker():
"""Create a marker for marking slow tests."""
return pytest.mark.skipif(
not pytest.config.getoption("--runslow", default=False),
reason="need --runslow option to run")
def assert_equal_contents(testCase, filename1, filename2):
'Assert contents of two files are equal for a unittest.TestCase'
testCase.assertTrue(filecmp.cmp(filename1, filename2, shallow=False))
def assert_equal_bam_reads(testCase, bam_filename1, bam_filename2):
import Bio.SeqIO
import pytest
# intra-project
import util.file
from util.misc import available_cpu_count
from tools.samtools import SamtoolsTool
logging.getLogger('botocore').setLevel(logging.WARNING)
logging.getLogger('boto3').setLevel(logging.WARNING)
if 'PYTEST_XDIST_WORKER_COUNT' in os.environ:
_CPUS = 1
else:
_CPUS = available_cpu_count()
def assert_equal_contents(testCase, filename1, filename2):
'Assert contents of two files are equal for a unittest.TestCase'
testCase.assertTrue(filecmp.cmp(filename1, filename2, shallow=False))
def assert_equal_bam_reads(testCase, bam_filename1, bam_filename2):
''' Assert that two bam files are equivalent
This function converts each file to sam (plaintext) format,
without header, since the header can be variable.
Test data should be stored in bam format rather than sam
to save space, and to ensure the bam->sam conversion