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)