"NA:i:4\tNH:i:4",
"NA:i:4\tNH:i:4",
"NA:i:4\tNH:i:4",
"NA:i:4\tNH:i:4"]
Read.process_set_sam_tag(sample, count_tag=True, tag_regex='NA:i:(\d+)')
Read.process_set_sam_tag(sample, count_tag=True, tag_regex='NH:i:(\d+)')
def test_build_positions():
for test in cigar_string:
yield (check_build_positions, test, cigar_string[test])
def check_build_positions(test, (values, expected)):
position_array = Read.build_positions(*values)
test_description = "\nTest: \t{}\n".format(test)
test_description += "Expected:\t{}\n".format(expected)
test_description += "Position:\t{}\n".format(position_array)
assert position_array == expected, "{}Error: \tDid not create the expected position array.".format(
test_description)
def test_catch_bad_cigar_input():
for test in bad_cigar_string:
yield (check_catch_bad_cigar_input, test, bad_cigar_string[test])
@raises(MetageneError)
def check_catch_bad_cigar_input(test, (values, expected)):
print Read.build_positions(*values)
"NA:i:4\tNH:i:4", "NA:i:4\tNH:i:4", "NA:i:4\tNH:i:4", "NA:i:4\tNH:i:4",
"NA:i:4\tNH:i:4", "NA:i:4\tNH:i:4", "NA:i:4\tNH:i:4", "NA:i:4\tNH:i:4",
"NA:i:4\tNH:i:4", "NA:i:4\tNH:i:4"
]
Read.process_set_sam_tag(sample, count_tag=True, tag_regex='NA:i:(\d+)')
Read.process_set_sam_tag(sample, count_tag=True, tag_regex='NH:i:(\d+)')
def test_build_positions():
for test in cigar_string:
yield (check_build_positions, test, cigar_string[test])
def check_build_positions(test, (values, expected)):
position_array = Read.build_positions(*values)
test_description = "\nTest: \t{}\n".format(test)
test_description += "Expected:\t{}\n".format(expected)
test_description += "Position:\t{}\n".format(position_array)
assert position_array == expected, "{}Error: \tDid not create the expected position array.".format(
test_description)
def test_catch_bad_cigar_input():
for test in bad_cigar_string:
yield (check_catch_bad_cigar_input, test, bad_cigar_string[test])
@raises(MetageneError)
def check_catch_bad_cigar_input(test, (values, expected)):
print Read.build_positions(*values)
