def test_skipped_zero_or_more(self):
tree = Tree(" ((((a, a, b)), (c, d), (e, f)), (g, h, i)) ; ")
pattern = TreePattern(" ( a, b, d*) ;")
result = (pattern.find_match(tree))
# false test
self.assertTrue(len(list(result)) == 0)
def test_skipped_zero_or_more(self):
tree = Tree(" ((((a, a, b)), (c, d), (e, f)), (g, h, i)) ; ")
pattern = TreePattern(" ( a, b, d*) ;")
result = (pattern.find_match(tree))
# false test
self.assertTrue(len(list(result)) == 0)
def test_constraintes_pattern(self):
tree = Tree(" ((((a, b)), (c, d), (e, f)), (g, h, i)) ; ")
(tree & 'a').dist = 0.2
(tree & 'b').dist = 0.4
(tree & 'c').dist = 0.5
(tree & 'd').dist = 0.6
(tree & 'e').dist = 0.7
(tree & 'f').dist = 0.8
(tree & 'g').dist = 0.9
pattern = TreePattern(" ('@.dist > 0.5+'); ", quoted_node_names=True)
result = pattern.find_match(tree)
expected = [(tree & 'e').up, (tree & 'g').up]
found = True
count = 0
for node in result:
count += 1
found &= node in expected
found &= count == 2
self.assertTrue(found)
def test_constraintes_pattern(self):
tree = Tree(" ((((a, b)), (c, d), (e, f)), (g, h, i)) ; ")
(tree&'a').dist = 0.2
(tree&'b').dist = 0.4
(tree&'c').dist = 0.5
(tree&'d').dist = 0.6
(tree&'e').dist = 0.7
(tree&'f').dist = 0.8
(tree&'g').dist = 0.9
pattern = TreePattern(" ('@.dist > 0.5+'); ", quoted_node_names=True)
result = pattern.find_match(tree)
expected = [(tree&'e').up, (tree&'g').up]
found = True
count = 0
for node in result:
count += 1
found &= node in expected
found &= count == 2
self.assertTrue(found)
def test_simple_plus(self):
tree = Tree(" (((a, a, b, qq), (a, b, c, ww)), (b, b, a, ee));", format=8)
pattern = TreePattern(" (qq, a+)^ ;")
result = pattern.find_match(tree)
expected = (tree&'qq').up
self.assertTrue(len(list(result)) > 0 )
def test_double_match(self):
tree = Tree(" (((a, a, b), (c, c, d) ), (e, e, f), (g, h, i)) ; ")
pattern = TreePattern(" ((a+, b)^, (e+, f)^);")
result = (pattern.find_match(tree))
#self.assertTrue(len(list(result)) > 0 )
self.assertEqual(next(result), tree)
def test_double_match(self):
tree = Tree(" (((a, a, b), (c, c, d) ), (e, e, f), (g, h, i)) ; ")
pattern = TreePattern( " ((a+, b)^, (e+, f)^);")
result = (pattern.find_match(tree))
#self.assertTrue(len(list(result)) > 0 )
self.assertEqual(next(result), tree)
def test_simple_plus(self):
tree = Tree(" (((a, a, b, qq), (a, b, c, ww)), (b, b, a, ee));",
format=8)
pattern = TreePattern(" (qq, a+)^ ;")
result = pattern.find_match(tree)
expected = (tree & 'qq').up
self.assertTrue(len(list(result)) > 0)
def test_simple_complete_topology(self):
pattern = TreePattern("((e, i, f)d)^ ; ")
true_match = [8, 9]
match = []
for num, tree in enumerate(self.trees):
result = pattern.find_match(tree)
if (len(list(result)) > 0):
match += [num + 1]
self.assertTrue(true_match == match)
def test_simple_complete_topology(self):
pattern = TreePattern("((e, i, f)d)^ ; ")
true_match = [8, 9]
match = []
for num, tree in enumerate(self.trees):
result = pattern.find_match(tree)
if (len(list(result)) > 0):
match += [num+1]
self.assertTrue(true_match == match)
def test_star_and_logical_constraints(self):
tree = Tree(" (((a, b), (c, d), (e, f)), (g, h, i)) ; ")
(tree&'a').dist = 0.2
(tree&'b').dist = 0.4
(tree&'c').dist = 0.5
(tree&'d').dist = 0.6
(tree&'e').dist = 0.7
(tree&'f').dist = 0.8
(tree&'g').dist = 0.9
pattern = TreePattern(""" ('g', '@.dist == 1+', 'fls_node*'); """, quoted_node_names=True)
result = pattern.find_match(tree)
self.assertEqual(next(result), (tree&'g').up)
def test_star_and_logical_constraints(self):
tree = Tree(" (((a, b), (c, d), (e, f)), (g, h, i)) ; ")
(tree & 'a').dist = 0.2
(tree & 'b').dist = 0.4
(tree & 'c').dist = 0.5
(tree & 'd').dist = 0.6
(tree & 'e').dist = 0.7
(tree & 'f').dist = 0.8
(tree & 'g').dist = 0.9
pattern = TreePattern(""" ('g', '@.dist == 1+', 'fls_node*'); """,
quoted_node_names=True)
result = pattern.find_match(tree)
self.assertEqual(next(result), (tree & 'g').up)
def test_constraints_and_loose(self):
tree = Tree(" (((((a, b), (c, d), (e, f)), (g, h, i)))) ; ")
(tree&'a').dist = 0.2
(tree&'b').dist = 0.4
(tree&'c').dist = 0.5
(tree&'d').dist = 0.6
(tree&'e').dist = 0.7
(tree&'f').dist = 0.7
(tree&'g').dist = 0.9
pattern = TreePattern(""" ('@.dist == 0.2', 'b')'^', ('@.dist > 0.5', '@.dist == 0.7+')'^' ; """, quoted_node_names=True)
result = pattern.find_match(tree)
res = next(result)
#self.assertEqual(res, ((tree&'f').up).up)
self.assertTrue( len(list(result)) > 0 )
def test_constraints_and_loose(self):
tree = Tree(" (((((a, b), (c, d), (e, f)), (g, h, i)))) ; ")
(tree & 'a').dist = 0.2
(tree & 'b').dist = 0.4
(tree & 'c').dist = 0.5
(tree & 'd').dist = 0.6
(tree & 'e').dist = 0.7
(tree & 'f').dist = 0.7
(tree & 'g').dist = 0.9
pattern = TreePattern(
""" ('@.dist == 0.2', 'b')'^', ('@.dist > 0.5', '@.dist == 0.7+')'^' ; """,
quoted_node_names=True)
result = pattern.find_match(tree)
res = next(result)
#self.assertEqual(res, ((tree&'f').up).up)
self.assertTrue(len(list(result)) > 0)
def test_exact_number_and_topology(self):
tree = Tree(" ((a, a, b)p1, ((c, c, c, d)p2, (e, f, g)p3)p4)p5 ;",
format=1)
p1 = TreePattern(" ('a{2,2}', 'b')'p1' ;", quoted_node_names=True)
p2 = TreePattern(" ('c{1,5}', 'd')'p2' ;", quoted_node_names=True)
p3 = TreePattern(" ('c{2,3}', d, 'ww{0,3}')p2 ;")
p4 = TreePattern(" ('c{3,3}', 'd{0,5}', 'ww{0,3}')p2;")
p5 = TreePattern(" ('c{1,2}', 'd{0,1}', 'ww*')p2;")
patterns = [p1, p2, p3, p4, p5]
true_match = [True, True, True, True, False]
match = True
for num, pattern in enumerate(patterns):
result = pattern.find_match(tree)
found = len(list(result)) > 0
match &= found == true_match[num]
self.assertTrue(match)
def test_two_terminal_nodes(self):
# The presense of leaves e, f as sister nodes.
pattern = TreePattern(" (e, f)^; ")
true_match = [4, 5, 6, 7, 8, 9, 10, 11]
matches = []
for num, tree in enumerate(self.trees):
one_use = deepcopy(pattern)
result = one_use.find_match(tree)
try:
res = next(result)
except:
res = None
if res:
matches += [num + 1]
self.assertTrue(matches == true_match)
def test_one_terminal_node(self):
# The c node exists as leaf (not internal)
pattern = TreePattern(" (c)^; ")
true_match = [1, 2, 3, 4, 5, 6]
matches = []
for num, tree in enumerate(self.trees):
one_use = deepcopy(pattern)
result = one_use.find_match(tree)
try:
res = next(result)
except:
res = None
if res:
matches += [num + 1]
self.assertTrue(matches == true_match)
def test_exact_number_of_repeat(self):
tree = Tree(
"((a, a, a, b, c), (d, d, qq), (e, e, e, ww, e, e, e, e, e)); ")
p1 = TreePattern(" (b, c, 'a{1,3}') ;")
p2 = TreePattern(" (b, c, 'a{2,3}') ;")
p3 = TreePattern(" (b, c, 'a{3,3}') ;")
p4 = TreePattern(" (b, c, 'a{4,5}') ;")
p5 = TreePattern(" (ww, 'e{1,8}') ;")
p6 = TreePattern(" (ww, 'e{7,9}') ;")
p7 = TreePattern(" (ww, 'e{1,3}') ;")
patterns = [p1, p2, p3, p4, p5, p6, p7]
true_match = [True, True, True, False, True, True, False]
match = True
for num, pattern in enumerate(patterns):
result = pattern.find_match(tree)
found = len(list(result)) > 0
match &= found == true_match[num]
self.assertTrue(match)
def test_simple_parent_two_children_false(self):
tree = Tree(" (((b, c)a, (b, c)a), (e, f)d) ;", format=1)
pattern = TreePattern("(b,c)qq ;")
result = pattern.find_match(tree)
self.assertTrue(len(list(result)) == 0)
def test_all(self):
test = True
t1 = Tree(" ((a, a, b)p1, ((c, c, c, d)p2, (e, f, g)p3)p4)p5 ;",
format=1)
p1 = TreePattern(" ('c+', 'd')'p2' ;", quoted_node_names=True)
test &= len(list(p1.find_match(t1))) > 0
# Should match
t1 = Tree(" (((F, G)E, (C, D)B), A);", format=8)
p1 = TreePattern("('@.support > 0', '@.support > 0')'B' ;")
test &= len(list(p1.find_match(t1))) > 0
# Should NOT match
t1 = Tree(" (((F, G)E, (C, D)B), A);", format=8)
p1 = TreePattern("('@.support > 0', '@.support > 0{2,3}')'B' ;")
test &= len(list(p1.find_match(t1))) == 0
# Should match
t1 = Tree(" (((F, G)E, (C, D)B), A);", format=8)
p1 = TreePattern("('C', '@.support > 0')'B' ;")
test &= len(list(p1.find_match(t1))) > 0
# Should not match
t1 = Tree("(((A, A, A), (B,C)), K);")
p1 = TreePattern("(((A, A+, A, A), (B,C)), K);")
test &= len(list(p1.find_match(t1))) == 0
# Should match
t1 = Tree("(((A, A, A), (B,C)), K);")
p1 = TreePattern("(((A, A+, A), (B,C)), K);")
test &= len(list(p1.find_match(t1))) > 0
# Should match
t1 = Tree("(((A, A, A), (B,C)), K);")
p1 = TreePattern("(((A, A+), (B,C)), K);")
test &= len(list(p1.find_match(t1))) > 0
# ^ after a ) means that the two children of that node can be connected by
# any number of internal up/down nodes
t1 = Tree("( ((B,Z), (D,F)), G);")
p1 = TreePattern("( (B,Z), G)^;")
test &= len(list(p1.find_match(t1))) > 0
t1 = Tree("( ((G, ((B,Z),A)), (D,G)), C);")
p1 = TreePattern("(((B,Z)^,C), G)^;")
test &= len(list(p1.find_match(t1))) == 0
t1 = Tree("( ((G, ((B,Z),A)), (D,G)), C);")
p1 = TreePattern("(((B,Z)^,G), C)^;")
test &= len(list(p1.find_match(t1))) > 0
t1 = Tree("(((A, (B,C,D)), ((B,C), A)), F);")
p1 = TreePattern("((C,B,D*), A);")
test &= len(list(p1.find_match(t1))) > 0
t1 = Tree("(((A, (B,C,D, D, D)), ((B,C), A)), F);")
p1 = TreePattern("((C,B,'D{2,3}'), A);")
test &= len(list(p1.find_match(t1))) > 0
t1 = Tree("(a, b, b, a);")
p1 = TreePattern("(a+, b+);")
test &= len(list(p1.find_match(t1))) > 0
t1 = Tree("((a, b), c);")
p1 = TreePattern("((a, b, d*), c);")
test &= len(list(p1.find_match(t1))) > 0
t1 = Tree("( (((B,H), (B,B,H), C), A), (K, J));")
p1 = TreePattern("((C, (B+,H)+), A);")
test &= len(list(p1.find_match(t1))) > 0
self.assertTrue(test)
def test_all(self):
test = True
t1 = Tree(" ((a, a, b)p1, ((c, c, c, d)p2, (e, f, g)p3)p4)p5 ;", format=1)
p1 = TreePattern(" ('c+', 'd')'p2' ;",quoted_node_names=True)
test &= len(list(p1.find_match(t1))) > 0
# Should match
t1 = Tree(" (((F, G)E, (C, D)B), A);", format=8)
p1 = TreePattern("('@.support > 0', '@.support > 0')'B' ;")
test &= len(list(p1.find_match(t1))) > 0
# Should NOT match
t1 = Tree(" (((F, G)E, (C, D)B), A);", format=8)
p1 = TreePattern("('@.support > 0', '@.support > 0{2,3}')'B' ;")
test &= len(list(p1.find_match(t1))) == 0
# Should match
t1 = Tree(" (((F, G)E, (C, D)B), A);", format=8)
p1 = TreePattern("('C', '@.support > 0')'B' ;")
test &= len(list(p1.find_match(t1))) > 0
# Should not match
t1 = Tree("(((A, A, A), (B,C)), K);")
p1 = TreePattern("(((A, A+, A, A), (B,C)), K);")
test &= len(list(p1.find_match(t1))) == 0
# Should match
t1 = Tree("(((A, A, A), (B,C)), K);")
p1 = TreePattern("(((A, A+, A), (B,C)), K);")
test &= len(list(p1.find_match(t1))) > 0
# Should match
t1 = Tree("(((A, A, A), (B,C)), K);")
p1 = TreePattern("(((A, A+), (B,C)), K);")
test &= len(list(p1.find_match(t1))) > 0
# ^ after a ) means that the two children of that node can be connected by
# any number of internal up/down nodes
t1 = Tree("( ((B,Z), (D,F)), G);")
p1 = TreePattern("( (B,Z), G)^;")
test &= len(list(p1.find_match(t1))) > 0
t1 = Tree("( ((G, ((B,Z),A)), (D,G)), C);")
p1 = TreePattern("(((B,Z)^,C), G)^;")
test &= len(list(p1.find_match(t1))) == 0
t1 = Tree("( ((G, ((B,Z),A)), (D,G)), C);")
p1 = TreePattern("(((B,Z)^,G), C)^;")
test &= len(list(p1.find_match(t1))) > 0
t1 = Tree("(((A, (B,C,D)), ((B,C), A)), F);")
p1 = TreePattern("((C,B,D*), A);")
test &= len(list(p1.find_match(t1))) > 0
t1 = Tree("(((A, (B,C,D, D, D)), ((B,C), A)), F);")
p1 = TreePattern("((C,B,'D{2,3}'), A);")
test &= len(list(p1.find_match(t1))) > 0
t1 = Tree("(a, b, b, a);")
p1 = TreePattern("(a+, b+);")
test &= len(list(p1.find_match(t1))) > 0
t1 = Tree("((a, b), c);")
p1 = TreePattern("((a, b, d*), c);")
test &= len(list(p1.find_match(t1))) > 0
t1 = Tree("( (((B,H), (B,B,H), C), A), (K, J));")
p1 = TreePattern("((C, (B+,H)+), A);")
test &= len(list(p1.find_match(t1))) > 0
self.assertTrue(test)
def run(args):
# a list of stats objects. one for every pattern
all_stats = []
if vars(args)["src_trees"] is None and vars(args)["src_tree_list"] is None:
logging.error('Please specify a tree to search (i.e. -t) ')
sys.exit(-1)
if not vars(args)["pattern_trees"] and not vars(args)["pattern_tree_list"]:
logging.error('Please specify a pattern to search for. (i.e. -p)')
sys.exit(-1)
pattern_length = len(list(pattern_tree_iterator(args)))
for pattern_num, p in enumerate(pattern_tree_iterator(args)):
try :
pattern = TreePattern(p, quoted_node_names=vars(args)["quoted_node_names"])
except:
logging.error("Could not create pattern from newick.")
continue
stats = match_stats("pattern_" + str(pattern_num))
# handle file creation
if vars(args)["output"]:
filename = vars(args)["output"]
if pattern_length > 1:
if '.' in vars(args)["output"]:
filename = filename.replace('.', str(pattern_num) + '.')
else:
filename += str(pattern_num)
outputfile = open(filename, 'w')
if vars(args)["verbosity"] and int(vars(args)["verbosity"][0]) > 2:
print("pattern_{} is: ".format(pattern_num))
print(pattern)
# for every tree
if vars(args)["verbosity"] and vars(args)["verbosity"][0] > 2 and not vars(args)["output"]:
print("match(es) for pattern_{}:".format(pattern_num))
for n, nw in enumerate(src_tree_iterator(args)):
stats.total += 1
try:
t = PhyloTree(nw, format=args.tree_format)
except:
logging.error("Could not creat tree from newick format.")
stats.errors += 1
continue
matches = list(pattern.find_match(t))
match_length=len(matches)
if match_length > 0:
stats.matched += 1
else:
stats.not_matched += 1
if args.render:
image = args.render
if vars(args)["whole_tree"]:
if pattern_length > 1: # multiple patterns
if '.' in image:
image = image.replace('.', str(pattern_num) + '.')
else:
image += str(pattern_num)
ts = TreeStyle()
ts.show_leaf_name = True
for n in t.traverse():
nstyle = NodeStyle()
if n in matches:
nstyle["fgcolor"] = "green"
nstyle["size"] = 7
else:
nstyle["fgcolor"] = "red"
nstyle["size"] = 5
n.set_style(nstyle)
t.render(image, tree_style=ts, layout=lambda x: None)
else:
if pattern_length > 1: # multiple patterns
if match_length > 1: # one file per match on each pattern
for m, match in enumerate(matches):
if '.' in image:
image = image.replace('.', str(pattern_num) + '_' + str(m) + '.')
else:
image += str(pattern_num) + str(m)
match.render(image)
elif match_length == 1: # One match on multiple patterns
if '.' in image:
image = image.replace('.', str(pattern_num) + '.')
else:
image += str(pattern_num)
matches[0].render(image)
else:
if vars(args)["verbosity"] and vars(args)["verbosity"][0] > 1:
print("No matches for pattern {} tree {}".format(pattern_num, n))
else: # one pattern
if match_length > 1: # one file per match on one pattern
for m, match in enumerate(matches):
if '.' in image:
image = image.replace('.', '_' + str(m) + '.')
else:
image += str(m)
match.render(image)
elif match_length == 1: # one file for one match
matches[0].render(image)
else:
if vars(args)["verbosity"] and vars(args)["verbosity"][0] > 1:
print("No matches for tree {}".format(n))
if vars(args)["output"]:
if vars(args)["asciioutput"]:
if vars(args)["whole_tree"] and match_length > 0:
outputfile.write(str(t))
else:
for match in matches:
outputfile.write(str(match) + '\n')
else: #args.taboutput
if vars(args)["whole_tree"]:
outputfile.whrite(t.write(features=[]))
else:
outputfile.write('\t'.join([match.write(features=[]) for match in matches]))
if not vars(args)["output"] and not args.render:
if vars(args)["asciioutput"]:
if vars(args)["whole_tree"] and match_length > 0:
print(t)
else:
for match in matches:
print(match)
else:
if vars(args)["whole_tree"] and match_length > 0:
print(t.write(features=[]))
else:
for match in matches:
print(match.write(features=[]))
all_stats += [stats]
if vars(args)["verbosity"] and vars(args)["verbosity"][0] > 3:
print("{}".format(stats))
if vars(args)["output"]:
outputfile.close()
concentrated = match_stats("\nSummarize")
concentrated.total = sum([ stat.total for stat in all_stats])
concentrated.num_of_patterns = len(all_stats)
concentrated.num_of_trees = concentrated.total / concentrated.num_of_patterns
concentrated.matched = sum([stat.matched for stat in all_stats])
concentrated.not_matched = sum([stat.not_matched for stat in all_stats])
concentrated.errors = sum([stat.errors for stat in all_stats])
if vars(args)["verbosity"] and vars(args)["verbosity"][0] > 1:
print("{}".format(concentrated))
def test_simple_parent_two_children_false(self):
tree = Tree(" (((b, c)a, (b, c)a), (e, f)d) ;", format=1)
pattern = TreePattern("(b,c)qq ;")
result = pattern.find_match(tree)
self.assertTrue(len(list(result)) == 0)