def test_check_fix(self):
'''test fix'''
infile = os.path.join(data_dir, 'refcheck_test_fix_in.fa')
tmp_prefix = 'tmp.refcheck_test_fix.out'
c = refcheck.Checker(infile, min_length=10, max_length=25)
c.fix(tmp_prefix)
for x in ['fa', 'log', 'rename', 'removed.fa']:
expected = os.path.join(data_dir, 'refcheck_test_fix_out.' + x)
got = tmp_prefix + '.' + x
self.assertTrue(filecmp.cmp(expected, got, shallow=False))
os.unlink(got)
def test_check_file_fail_too_long(self):
'''test check file fail long gene'''
infile = os.path.join(data_dir, 'refcheck_test_check_too_long.fa')
c = refcheck.Checker(infile, max_length=6)
seq = pyfastaq.sequences.Fasta('gene1', 'TTGTGGTGA')
self.assertEqual(c.check(), (False, 'Too long', seq))
def test_check_file_fail_not_gene(self):
'''test check file fail not a gene'''
infile = os.path.join(data_dir, 'refcheck_test_check_not_gene.fa')
c = refcheck.Checker(infile)
seq = pyfastaq.sequences.Fasta('gene1', 'TTGTGATGA')
self.assertEqual(c.check(), (False, 'Not a gene', seq))
def test_check_file_fail_too_short(self):
'''test check file fail short gene'''
infile = os.path.join(data_dir, 'refcheck_test_check_too_short.fa')
c = refcheck.Checker(infile, min_length=10)
seq = pyfastaq.sequences.Fasta('gene1', 'TTGTGGTGA')
self.assertEqual(c.check(), (False, 'Too short', seq))
def test_check_pass(self):
'''test check file OK'''
infile = os.path.join(data_dir, 'refcheck_test_check_ok.fa')
c = refcheck.Checker(infile)
self.assertEqual(c.check(), (True, None, None))