def test_split_db_split_fp_errors(self):
temp_dir = gettempdir()
self.to_delete.append(temp_dir)
with self.assertRaises(BadParameter):
split_db(self.bad_tax_fp, self.seqs_fp, 'Streptococcus', temp_dir,
None)
with self.assertRaises(BadParameter):
split_db(self.tax_fp, self.seqs_fp, None, temp_dir,
self.bad_split_fp)
def test_split_db_split_fp_errors(self):
temp_dir = gettempdir()
self.to_delete.append(temp_dir)
with self.assertRaises(BadParameter):
split_db(self.bad_tax_fp, self.seqs_fp, 'Streptococcus', temp_dir,
None)
with self.assertRaises(BadParameter):
split_db(self.tax_fp, self.seqs_fp, None, temp_dir,
self.bad_split_fp)
def test_split_db(self):
temp_dir = gettempdir()
self.to_delete.append(temp_dir)
split_db(self.tax_fp, self.seqs_fp, 'Streptococcus', temp_dir, None)
exp_interest = join(self.base, 'interest.fna')
exp_rest = join(self.base, 'rest.fna')
out_interest = join(temp_dir, 'interest.fna')
out_rest = join(temp_dir, 'rest.fna')
with open(exp_interest) as exp, open(out_interest) as out:
self.assertItemsEqual(exp.readlines(), out.readlines())
with open(exp_rest) as exp, open(out_rest) as out:
self.assertItemsEqual(exp.readlines(), out.readlines())
def test_split_db(self):
temp_dir = gettempdir()
self.to_delete.append(temp_dir)
split_db(self.tax_fp, self.seqs_fp, 'Streptococcus', temp_dir, None)
exp_interest = join(self.base, 'interest.fna')
exp_rest = join(self.base, 'rest.fna')
out_interest = join(temp_dir, 'interest.fna')
out_rest = join(temp_dir, 'rest.fna')
with open(exp_interest) as exp, open(out_interest) as out:
self.assertItemsEqual(exp.readlines(), out.readlines())
with open(exp_rest) as exp, open(out_rest) as out:
self.assertItemsEqual(exp.readlines(), out.readlines())
def test_split_db_split_fp(self):
temp_dir = gettempdir()
self.to_delete.append(temp_dir)
split_fp = join(self.base, 'split_fp.txt')
split_db(self.tax_fp, self.seqs_fp, None, temp_dir, split_fp)
exp_interest = join(self.base, 'split-interest.fna')
exp_rest = join(self.base, 'split-rest.fna')
out_interest = join(temp_dir, 'interest.fna')
out_rest = join(temp_dir, 'rest.fna')
with open(exp_interest) as exp, open(out_interest) as out:
self.assertItemsEqual(exp.readlines(), out.readlines())
with open(exp_rest) as exp, open(out_rest) as out:
self.assertItemsEqual(exp.readlines(), out.readlines())
def test_split_db_split_fp(self):
temp_dir = gettempdir()
self.to_delete.append(temp_dir)
split_fp = join(self.base, 'split_fp.txt')
split_db(self.tax_fp, self.seqs_fp, None, temp_dir, split_fp)
exp_interest = join(self.base, 'split-interest.fna')
exp_rest = join(self.base, 'split-rest.fna')
out_interest = join(temp_dir, 'interest.fna')
out_rest = join(temp_dir, 'rest.fna')
with open(exp_interest) as exp, open(out_interest) as out:
self.assertItemsEqual(exp.readlines(), out.readlines())
with open(exp_rest) as exp, open(out_rest) as out:
self.assertItemsEqual(exp.readlines(), out.readlines())
def test_split_db_no_results(self):
with self.assertRaises(BadParameter):
split_db(self.tax_fp, self.seqs_fp, ":L doesn't exist", 'output',
None)
def test_split_db_no_results(self):
with self.assertRaises(BadParameter):
split_db(self.tax_fp, self.seqs_fp, ":L doesn't exist", 'output',
None)
