def test_is_fastq():
good_name1 = "foo.fastq"
good_name2 = "bar.fastq.gz"
bad_name1 = "foo.fasta"
bad_name2 = "bar.fastq.baz"
assert_equal(provider_utils.is_fastq(good_name1), True)
assert_equal(provider_utils.is_fastq(good_name2), True)
assert_equal(provider_utils.is_fastq(bad_name1), False)
assert_equal(provider_utils.is_fastq(bad_name2), False)
def get_fastq_file_ending(self, filename):
"""Extract file ending from FASTQ filename"""
if utils.is_fastq(filename) is False:
raise ValueError("{0} is not a valid FASTQ file!".format(filename))
pattern = "^.*(\.fastq(\.gz)?)$"
match = search(pattern, filename)
return match.group(1)
def is_fastq(self, filename):
"""Check if file has FASTQ ending."""
return utils.is_fastq(filename)