def test_rename_files(self): for fn in ['sample_a.fastq.gz', 'sample_b.fastq.gz']: shutil.copy(self.fastq_fp, str(self.per_sample_dir_fmt.path / pathlib.Path(fn))) _rename_files(self.per_sample_dir_fmt, self.barcode_series) seqs = self.per_sample_dir_fmt.sequences.iter_views(FastqGzFormat) for fn, (sample_id, barcode) in zip(seqs, self.barcode_series.iteritems()): self.assertTrue(sample_id in str(fn)) self.assertTrue(barcode in str(fn))
def test_rename_files_extra_samples_in_barcode_map(self): barcode_series = pd.Series(['A', 'G', 'C'], index=['sample_a', 'sample_b', 'sample_c']) for fn in ['sample_a.fastq.gz', 'sample_b.fastq.gz']: shutil.copy(self.fastq_fp, str(self.per_sample_dir_fmt.path / pathlib.Path(fn))) _rename_files(self.per_sample_dir_fmt, barcode_series) seqs = self.per_sample_dir_fmt.sequences.iter_views(FastqGzFormat) for fn, (sample_id, barcode) in zip(seqs, barcode_series.iteritems()): self.assertTrue(sample_id in str(fn)) self.assertTrue(barcode in str(fn))
def test_rename_files(self): for fn in [ 'sample_a.1.fastq.gz', 'sample_a.2.fastq.gz', 'sample_b.1.fastq.gz', 'sample_b.2.fastq.gz' ]: shutil.copy(self.fastq_fp, str(self.per_sample_dir_fmt.path / pathlib.Path(fn))) _rename_files(self.seqs_dir_fmt, self.per_sample_dir_fmt, self.barcode_series) seqs = self.per_sample_dir_fmt.sequences.iter_views(FastqGzFormat) exp = [('sample_a', 'A'), ('sample_a', 'A'), ('sample_b', 'G'), ('sample_b', 'G')] counter = 0 for fn, (sample_id, barcode) in zip(seqs, exp): self.assertTrue(sample_id in str(fn)) self.assertTrue(barcode in str(fn)) counter += 1 self.assertEqual(counter, 4)