def test_estimate_read_filtering_params():
"""
--minMappingQuality 10 --samFlagExclude 512 --ignoreDuplicates -bl
"""
outfile = '/tmp/test_params.txt'
args = '-b {} --minMappingQuality 10 --samFlagExclude 512 --ignoreDuplicates -bl {} -o {}'.format(BAMFILE_FILTER, BEDFILE_FILTER, outfile).split()
est.main(args)
_foo = open(outfile, 'r')
resp = _foo.readlines()
_foo.close()
# strip the path from the output
_ = resp[1].split("\t")
_[0] = os.path.basename(_[0])
resp[1] = "\t".join(_)
expected = ['Sample\tTotal Reads\tMapped Reads\tAlignments in blacklisted regions\tEstimated mapped reads filtered\tBelow MAPQ\tMissing Flags\tExcluded Flags\tInternally-determined Duplicates\tMarked Duplicates\tSingletons\tWrong strand\n',
'test_filtering.bam\t193\t193\t7\t193\t41.4\t0.0\t186.5\t31.6\t0.0\t0.0\t0.0\n']
assert_equal(resp, expected)
unlink(outfile)
def test_estimate_read_filtering_minimal():
"""
Minimal testing
"""
outfile = '/tmp/test_minimal.txt'
args = '-b {} -o {}'.format(BAMFILE_FILTER, outfile).split()
est.main(args)
_foo = open(outfile, 'r')
resp = _foo.readlines()
_foo.close()
expected = [
'Sample\tTotal Reads\tMapped Reads\tAlignments in blacklisted regions\tEstimated mapped reads filtered\tBelow MAPQ\tMissing Flags\tExcluded Flags\tInternally-determined Duplicates\tMarked Duplicates\tSingletons\tWrong strand\n',
'test_filtering.bam\t193\t193\t0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n'
]
# strip the path from the output
_ = resp[1].split("\t")
_[0] = os.path.basename(_[0])
resp[1] = "\t".join(_)
assert_equal(resp, expected)
unlink(outfile)