def test_find_gembase_file_basename_file_not_in_gembase(self):
"""
test if find_gembase_file_basename get the the right basename
for files not located in gembase and file name is the output of split operation
a file containing one contig
a file representing a chunk
"""
gembase_path = self.find_data('Gembase')
file_names = {
'ACBA.0917.00019':
self.find_data(
os.path.join('Replicons', 'ACBA.0917.00019.0001.fst')),
'ESCO001.C.00001.C001.fst':
os.path.join(self.tmp_dir, 'ESCO001.C.00001.C001_chunk_1.fst')
}
shutil.copyfile(
os.path.join(gembase_path, 'Replicons',
'ESCO001.C.00001.C001.fst'),
file_names['ESCO001.C.00001.C001.fst'])
for base_file_name, replicon_path in file_names.items():
self.args.replicon = replicon_path
self.args.gembase_path = gembase_path
cfg = Config(self.args)
seq_db = read_multi_prot_fasta(replicon_path)
replicon = next(seq_db)
replicon.path = replicon_path
os.makedirs(cfg.tmp_dir(replicon.id))
with self.catch_log():
db = GembaseDB(replicon, cfg, gembase_path=gembase_path)
self.assertTrue(
db._find_gembase_file_basename(gembase_path, replicon_path),
base_file_name)
replicon_path = self.find_data(
os.path.join('Replicons', 'acba.007.p01.13.fst'))
self.args.replicon = replicon_path
self.args.gembase_path = gembase_path
cfg = Config(self.args)
seq_db = read_multi_prot_fasta(replicon_path)
replicon = next(seq_db)
replicon.path = replicon_path
os.makedirs(cfg.tmp_dir(replicon.id))
with self.assertRaises(FileNotFoundError) as ctx:
with self.catch_log():
GembaseDB(replicon, cfg, gembase_path=gembase_path)
self.assertEqual(
str(ctx.exception),
'cannot find lst file matching {} sequence'.format(replicon_path))
def test_find_gembase_file_basename_file_not_in_gembase(self):
"""
test if find_gembase_file_basename get the the right basename
for files not located in gembase and file name is the output of split operation
a file containing one contig
a file representing a chunk
"""
gembase_path = self.find_data('Gembase')
file_names = {'ACBA.0917.00019': self.find_data(os.path.join('Replicons', 'ACBA.0917.00019.0001.fst')),
'ESCO001.C.00001.C001.fst': os.path.join(self.tmp_dir, 'ESCO001.C.00001.C001_chunk_1.fst')
}
shutil.copyfile(os.path.join(gembase_path, 'Replicons', 'ESCO001.C.00001.C001.fst'),
file_names['ESCO001.C.00001.C001.fst'])
for base_file_name, replicon_path in file_names.items():
self.args.replicon = replicon_path
self.args.gembase_path = gembase_path
cfg = Config(self.args)
seq_db = read_multi_prot_fasta(replicon_path)
replicon = next(seq_db)
replicon.path = replicon_path
os.makedirs(cfg.tmp_dir(replicon.id))
with self.catch_log():
db = GembaseDB(replicon, cfg, gembase_path=gembase_path)
self.assertTrue(db._find_gembase_file_basename(gembase_path, replicon_path),
base_file_name)
replicon_path = self.find_data(os.path.join('Replicons', 'acba.007.p01.13.fst'))
self.args.replicon = replicon_path
self.args.gembase_path = gembase_path
cfg = Config(self.args)
seq_db = read_multi_prot_fasta(replicon_path)
replicon = next(seq_db)
replicon.path = replicon_path
os.makedirs(cfg.tmp_dir(replicon.id))
with self.assertRaises(FileNotFoundError) as ctx:
with self.catch_log():
GembaseDB(replicon, cfg, gembase_path=gembase_path)
self.assertEqual(str(ctx.exception),
'cannot find lst file matching {} sequence'.format(replicon_path))
def test_find_gembase_file_basename(self):
"""
test if find_gembase_file_basename get the the right basename
for files in gembase
"""
gembase_path = self.find_data('Gembase')
file_names = ('ACBA.0917.00019.fna', 'ESCO001.C.00001.C001.fst')
for file_name in file_names:
replicon_path = self.find_data(os.path.join('Gembase', 'Replicons', file_name))
self.args.replicon = replicon_path
cfg = Config(self.args)
seq_db = read_multi_prot_fasta(replicon_path)
replicon = next(seq_db)
replicon.path = replicon_path
os.makedirs(cfg.tmp_dir(replicon.id))
with self.catch_log():
db = GembaseDB(replicon, cfg)
self.assertTrue(db._find_gembase_file_basename(gembase_path, replicon_path),
os.path.splitext(file_name)[0])
def test_find_gembase_file_basename(self):
"""
test if find_gembase_file_basename get the the right basename
for files in gembase
"""
gembase_path = self.find_data('Gembase')
file_names = ('ACBA.0917.00019.fna', 'ESCO001.C.00001.C001.fst')
for file_name in file_names:
replicon_path = self.find_data(
os.path.join('Gembase', 'Replicons', file_name))
self.args.replicon = replicon_path
cfg = Config(self.args)
seq_db = read_multi_prot_fasta(replicon_path)
replicon = next(seq_db)
replicon.path = replicon_path
os.makedirs(cfg.tmp_dir(replicon.id))
with self.catch_log():
db = GembaseDB(replicon, cfg)
self.assertTrue(
db._find_gembase_file_basename(gembase_path, replicon_path),
os.path.splitext(file_name)[0])
