def test_read_rst(self):
# Extract branch information from rst file
infile = 'example_dataset/data/44/44.phy'
branches = SWAMP.read_rst(infile)
self.assertEqual(len(branches['5..7']), 6)
self.assertEqual(len(branches['5..6']), 0)
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_phylip(self):
infile = 'example_dataset/data/101/101.phy'
seq_dict = SWAMP.read_phylip(infile)
# read_phylip returns a dict
self.assertTrue(type(seq_dict) is dict)
# Dict contains 4 seqs
self.assertEqual(len(seq_dict.keys()), 4)
# Sequence length check.
self.assertEqual(len(seq_dict['pongo']), 1413)
# Try another file.
infile = 'example_dataset/data/44/44.phy'
seq_dict = SWAMP.read_phylip(infile)
self.assertEqual(len(seq_dict['pongo']), 1905)
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)
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_write_phylip(self):
infile = 'example_dataset/data/44/44.phy'
seq_dict = SWAMP.read_phylip(infile)
# Create some fake codons to mask.
codons_to_mask = {}
for i in range(2, 13):
codons_to_mask[i] = ['pongo', 'h**o']
# Write file...
masked_dict = SWAMP.mask_codons(seq_dict, codons_to_mask)
SWAMP.print_masked_phyfile(infile, masked_dict)
# Read it back
masked_file = 'example_dataset/data/44/44_masked.phy'
new_masked_dict = SWAMP.read_phylip(masked_file)
pongo_seq = new_masked_dict['pongo']
human_seq = new_masked_dict['h**o']
colobus_seq = new_masked_dict['colobus']
# Make sure we see the masked seqs
self.assertTrue(('NNN' * 10) in pongo_seq)
self.assertTrue(('NNN' * 10) in human_seq)
self.assertFalse(('NNN' * 10) in colobus_seq)
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)
