def test_get_fastq_files(self):
files = [
"1/P1234_1_TAGCTT_L001_R1_001.fastq.gz",
"1/P1234_1_TAGCTT_L001_R2_001.fastq.gz",
"1/P1234_1_TAGCTT_L002_R1_001.fastq.gz",
"1/P1234_1_TAGCTT_L002_R2_001.fastq.gz",
"2/P1234_2_TAGCTT_L001_R1_001.fastq.gz",
"2/P1234_2_TAGCTT_L001_R2_001.fastq.gz",
"2/P1234_2_TAGCTT_L002_R1_001.fastq.gz",
"2/P1234_2_TAGCTT_L002_R2_001.fastq.gz",
]
expected = [os.path.join(self.tmp_root, f) for f in files]
assert_equal(provider_utils.get_fastq_files(self.tmp_root), expected)
def get_samples(self):
"""Return a list of all Samples found in project root."""
files = utils.get_fastq_files(self.project_root)
return utils.get_samples(files, self)
def set_pattern(self, project_dir):
"""Set filename pattern."""
fastq_files = utils.get_fastq_files(project_dir)
self.pattern = self.get_first_matching_pattern(fastq_files)
