def test_sliding_window_scan(self):
infiles = ['example_dataset/data/44/44.phy']
threshold = 1
windowsize = 20
interscan = False
branch_file = 'example_dataset/branchcodes.txt'
branch_codes = SWAMP.read_branchcodes(branch_file)
# Run a sliding window scan on this single file.
SWAMP.sliding_window_scan(infiles, threshold, windowsize,
interscan, branch_codes)
# Check that the masked file exists and contains 'NNN's
masked_file = 'example_dataset/data/44/44_masked.phy'
masked_dict = SWAMP.read_phylip(masked_file)
pongo_seq = masked_dict['pongo']
self.assertTrue('NNN' in pongo_seq)
# Increase threshold, ensure NNNs are gone.
threshold = 10
SWAMP.sliding_window_scan(infiles, threshold, windowsize,
interscan, branch_codes)
masked_dict = SWAMP.read_phylip(masked_file)
pongo_seq = masked_dict['pongo']
self.assertFalse('NNN' in pongo_seq)
def test_read_branchcodes(self):
infile = 'example_dataset/branchcodes.txt'
branch_codes = SWAMP.read_branchcodes(infile)
# Branch codes come out like '5..7' -> (papio, colobus)
branch_a = branch_codes['5..7']
self.assertIn('papio', branch_a)
self.assertIn('colobus', branch_a)
# Single-species branch should have single-length array, e.g.
# '6..2' -> (human)
branch_b = branch_codes['6..2']
self.assertEqual(len(branch_b), 1)
def test_branch_error_check(self):
seq_file = 'example_dataset/data/44/44.phy'
seq_dict = SWAMP.read_phylip(seq_file)
branch_file = 'example_dataset/branchcodes.txt'
branch_codes = SWAMP.read_branchcodes(branch_file)
# No error raised when valid branch codes provided.
SWAMP.branch_error_check(branch_codes, seq_dict)
# Error is raised when branchcodes is not present
# (e.g. no file provided by user on command line)
with self.assertRaises(ValueError) as cm:
SWAMP.branch_error_check(None, seq_dict)
# Mess up one of the branch_codes, adding an unknown species
branch_codes['5..7'] += tuple(['gorilla'])
# Error is raised when species isn't found in seq_dict.
with self.assertRaises(ValueError) as cm:
SWAMP.branch_error_check(branch_codes, seq_dict)
def test_interscan(self):
infile = 'example_dataset/data/44/44.phy'
threshold = 1
windowsize = 10
interscan = False
branch_file = 'example_dataset/branchcodes.txt'
branch_codes = SWAMP.read_branchcodes(branch_file)
# Mask without interscan... fewer masked codons
result = SWAMP.sliding_window_scan_file(infile, threshold, windowsize,
interscan, branch_codes)
self.assertEqual(result['masked_column_count'], 215)
# Mask with interscan... more masked codons
interscan = True
result = SWAMP.sliding_window_scan_file(infile, threshold, windowsize,
interscan, branch_codes)
self.assertEqual(result['masked_column_count'], 301)