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)