def filter_samples(demux: _PlotQualView, metadata: Metadata,
where: str = None, exclude_ids: bool = False) \
-> CasavaOneEightSingleLanePerSampleDirFmt:
results = CasavaOneEightSingleLanePerSampleDirFmt()
paired = demux.paired
samples = demux.directory_format
ids_to_keep = metadata.get_ids(where=where)
if not ids_to_keep:
raise ValueError('No filtering requested.')
manifest = samples.manifest.view(pd.DataFrame)
if exclude_ids:
ids_to_keep = set(manifest.index) - set(ids_to_keep)
try:
for id in ids_to_keep:
forward = manifest.loc[id].forward
duplicate(forward,
os.path.join(str(results),
os.path.split(forward)[1]))
if paired:
reverse = manifest.loc[id].reverse
duplicate(
reverse,
os.path.join(str(results),
os.path.split(reverse)[1]))
except KeyError:
raise ValueError(f'{id!r} is not a sample present in the '
'demultiplexed data.')
return results
def test_perm_error_EPERM(self, mocked_link):
util.duplicate(self.src, self.dst1)
assert mocked_link.called
assert os.path.exists(self.dst1)
with open(self.dst1) as fh:
self.assertEqual(fh.read(), SECRET)
def test_cross_device_perm_error(self, mocked_link, mocked_copyfile):
with self.assertRaisesRegex(
PermissionError, "insufficient r/w permissions"):
util.duplicate(self.src, self.dst1)
assert mocked_link.called
assert mocked_copyfile.called
def test_perm_error_EPERM(self, mocked_link):
util.duplicate(self.src, self.dst1)
assert mocked_link.called
assert os.path.exists(self.dst1)
with open(self.dst1) as fh:
self.assertEqual(fh.read(), SECRET)
def test_cross_device_dst_not_exists(self, mocked_link):
util.duplicate(self.src, self.dst1)
assert mocked_link.called
assert os.path.exists(self.dst1)
with open(self.dst1) as fh:
self.assertEqual(fh.read(), SECRET)
def test_cross_device_perm_error(self, mocked_link, mocked_copyfile):
with self.assertRaisesRegex(
PermissionError, "insufficient r/w permissions"):
util.duplicate(self.src, self.dst1)
assert mocked_link.called
assert mocked_copyfile.called
def test_cross_device_dst_not_exists(self, mocked_link):
util.duplicate(self.src, self.dst1)
assert mocked_link.called
assert os.path.exists(self.dst1)
with open(self.dst1) as fh:
self.assertEqual(fh.read(), SECRET)
def setup_database_dir(tmpdir, database, refseqs, reftaxa):
BOWTIE_PATH = 'bowtie2'
duplicate(str(refseqs), os.path.join(tmpdir, 'refseqs.fna'))
reftaxa.to_csv(os.path.join(tmpdir, 'taxa.tsv'), sep='\t')
shutil.copytree(str(database),
os.path.join(tmpdir, BOWTIE_PATH),
copy_function=duplicate)
# 'bowtie2': os.path.join(BOWTIE_PATH, database.get_name())
bowtie_filename = glob.glob(str(database) + '/*.rev.1.bt2')
if not bowtie_filename:
raise Exception("Couldn't find bowtie index files at %s" %
(str(database)))
bowtie_basename = bowtie_filename[0].split('/')[-1].replace(
'.rev.1.bt2', '')
params = {
'general': {
'taxonomy': 'taxa.tsv',
'fasta': 'refseqs.fna'
},
#'bowtie2': os.path.join(BOWTIE_PATH, 'genomes.small')
'bowtie2': os.path.join(BOWTIE_PATH, bowtie_basename)
}
with open(os.path.join(tmpdir, 'metadata.yaml'), 'w') as fh:
yaml.dump(params, fh, default_flow_style=False)
def setup_database_dir(tmpdir, database, refseqs, reftaxa):
BOWTIE_PATH = 'bowtie2'
duplicate(str(refseqs), os.path.join(tmpdir, 'refseqs.fna'))
reftaxa.to_csv(os.path.join(tmpdir, 'taxa.tsv'), sep='\t')
shutil.copytree(str(database), os.path.join(tmpdir, BOWTIE_PATH),
copy_function=duplicate)
params = {
'general': {
'taxonomy': 'taxa.tsv',
'fasta': 'refseqs.fna'
},
'bowtie2': os.path.join(BOWTIE_PATH, database.get_basename())
}
with open(os.path.join(tmpdir, 'metadata.yaml'), 'w') as fh:
yaml.dump(params, fh, default_flow_style=False)
def test_cross_device_dst_exists(self, mocked_link):
with self.assertRaisesRegex(FileExistsError, self.dst2):
util.duplicate(self.src, self.dst2)
def test_cross_device_src_not_exists(self, mocked_link):
with self.assertRaisesRegex(FileNotFoundError, self.missing):
util.duplicate(self.missing, self.dst1)
def test_perm_error_EACCES(self, mocked_link):
with self.assertRaisesRegex(
PermissionError, "insufficient r/w permissions"):
util.duplicate(self.src, self.dst1)
assert mocked_link.called
def test_dst_dir(self):
with self.assertRaisesRegex(IsADirectoryError, self.dir):
util.duplicate(self.src, self.dir)
def test_perm_error(self, mocked_link):
with self.assertRaisesRegex(PermissionError, "find this"):
util.duplicate(self.src, self.dst1)
assert mocked_link.called
def test_cross_device_src_not_exists(self, mocked_link):
with self.assertRaisesRegex(FileNotFoundError, self.missing):
util.duplicate(self.missing, self.dst1)
def test_dst_exists(self):
with self.assertRaisesRegex(FileExistsError, self.dst2):
util.duplicate(self.src, self.dst2)
def test_src_not_exists(self):
with self.assertRaisesRegex(FileNotFoundError, self.missing):
util.duplicate(self.missing, self.dst1)
def test_src_not_exists(self):
with self.assertRaisesRegex(FileNotFoundError, self.missing):
util.duplicate(self.missing, self.dst1)
def test_dst_not_exists(self):
util.duplicate(self.src, self.dst1)
assert os.path.exists(self.dst1)
with open(self.dst1) as fh:
self.assertEqual(fh.read(), SECRET)
def test_perm_error_EACCES(self, mocked_link):
with self.assertRaisesRegex(
PermissionError, "insufficient r/w permissions"):
util.duplicate(self.src, self.dst1)
assert mocked_link.called
def test_dst_exists(self):
with self.assertRaisesRegex(FileExistsError, self.dst2):
util.duplicate(self.src, self.dst2)
def test_cross_device_dst_exists(self, mocked_link):
with self.assertRaisesRegex(FileExistsError, self.dst2):
util.duplicate(self.src, self.dst2)
def test_dst_dir(self):
with self.assertRaisesRegex(IsADirectoryError, self.dir):
util.duplicate(self.src, self.dir)
def test_cross_device_dst_dir(self, mocked_link):
with self.assertRaisesRegex(IsADirectoryError, self.dir):
util.duplicate(self.src, self.dir)
def test_dst_not_exists(self):
util.duplicate(self.src, self.dst1)
assert os.path.exists(self.dst1)
with open(self.dst1) as fh:
self.assertEqual(fh.read(), SECRET)
def test_cross_device_dst_dir(self, mocked_link):
with self.assertRaisesRegex(IsADirectoryError, self.dir):
util.duplicate(self.src, self.dir)
def test_perm_error(self, mocked_link):
with self.assertRaisesRegex(PermissionError, "find this"):
util.duplicate(self.src, self.dst1)
assert mocked_link.called
