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)