def test_findall(self):
"""find all files recursively"""
found = list(io_app.findall(self.basedir, suffix=".fasta"))
self.assertTrue(len(found) > 1)
found = list(io_app.findall(self.basedir, suffix=".fasta", limit=2))
self.assertTrue(len(found) == 2)
# and with a suffix
found = list(io_app.findall(self.basedir, suffix=".fasta*"))
self.assertTrue(len(found) > 2)
def test_write_seqs(self):
"""correctly writes sequences out"""
fasta_paths = list(io_app.findall(self.basedir, suffix=".fasta", limit=2))
fasta_loader = io_app.load_aligned(format="fasta")
alns = list(map(fasta_loader, fasta_paths))
with TemporaryDirectory(dir=".") as dirname:
writer = io_app.write_seqs(dirname, if_exists="ignore")
wrote = list(map(writer, alns))
written = list(io_app.findall(dirname, suffix="fasta"))
for i, wrote in enumerate(written):
self.assertEqual(alns[i].info.stored, join(dirname, wrote))
def test_findall_zip(self):
"""find all files recursively in a zip archive"""
with TemporaryDirectory(dir=".") as dirname:
zip_path = join(dirname, "new")
shutil.make_archive(zip_path, "zip", self.basedir)
zip_path = zip_path + ".zip" # because shutil adds the suffix
found = list(io_app.findall(zip_path, suffix="fasta"))
self.assertTrue(len(found) > 1)
found = list(io_app.findall(zip_path, suffix="fasta", limit=2))
self.assertTrue(len(found) == 2)
# and with a suffix
found = list(io_app.findall(zip_path, suffix=".fasta*"))
self.assertTrue(len(found) > 2)
def test_load_aligned_from_zip(self):
"""correctly loads aligned seqs from a zip archive"""
def validate(paths, loader):
loaded = list(map(loader, paths))
for i, aln in enumerate(loaded):
self.assertTrue(len(aln) > 10)
self.assertIsInstance(aln, ArrayAlignment)
# paths is only the basename when workjing with zip archives
# whereas the inpath will have full path of zip archive
self.assertEqual(aln.info.source, paths[i])
self.assertEqual(aln.info.source, paths[i])
with TemporaryDirectory(dir=".") as dirname:
zip_path = join(dirname, self.basedir.replace(".zip", ""))
shutil.make_archive(
base_name=zip_path, root_dir=".", format="zip", base_dir=self.basedir
)
zip_path = zip_path + ".zip" # because shutil adds the suffix
fasta_paths = list(io_app.findall(zip_path, suffix=".fasta", limit=2))
fasta_loader = io_app.load_aligned(format="fasta")
validate(fasta_paths, fasta_loader)
