def test_generic_readwrite(self):
expected = """Begin data;
Dimensions ntax=4 nchar=2;
Format datatype=standard symbols="01" gap=-;
Matrix
Harry 00
Simon 01
Betty 10
Louise 11
;
""".split("\n")
nex = NexusReader()
nex.handlers['data'] = GenericHandler
nex.read_file(os.path.join(EXAMPLE_DIR, 'example.nex'))
for line in nex.data.write().split("\n"):
e = expected.pop(0).strip()
assert line.strip() == e
def test_generic_readwrite(self):
expected = """Begin data;
Dimensions ntax=4 nchar=2;
Format datatype=standard symbols="01" gap=-;
Matrix
Harry 00
Simon 01
Betty 10
Louise 11
;
""".split("\n")
nex = NexusReader()
nex.handlers['data'] = GenericHandler
nex.read_file(os.path.join(EXAMPLE_DIR, 'example.nex'))
for line in nex.data.write().split("\n"):
e = expected.pop(0).strip()
assert line.strip() == e
from nexus import NexusReader
from Bio import SeqIO
import sys
n = NexusReader()
n.read_file("Razafimandimbison_AppS1.txt")
for taxon,characters in n.data:
print(">",taxon)
print("".join(characters)[7865:10693])
fasta_in = "Psychotria_trn.fas" #fastaファイルを読みこみ
for record in SeqIO.parse(fasta_in, 'fasta'):
id_part = record.id
desc_part = record.description
seq = record.seq
print('>', id_part)
print(seq)
class TreeParser(object):
START = 1
END = 2
NODE = 3
COMMA = 4
ANNOTATION = 5
BRANCH = 6
taxa_re = re.compile(r"([A-Za-z0-9_\-\.]+)")
branch_re = re.compile(r"(\d+(?:\.\d+))")
def __init__(self, path):
self.n = NexusReader()
self.n.read_file(path)
def parse(self, _id):
data = self.n.trees.trees[_id]
tokens = self._tokenize(data)
return self._parse(tokens)
def _tokenize(self, data):
tree_data = data[data.find(
'('):-1] # skip tree-level annotation & strip the last semicolon
idx = 0
tokens = []
while idx < len(tree_data):
if tree_data[idx] == '(':
tokens.append(self.START)
idx += 1
elif tree_data[idx] == ')':
tokens.append(self.END)
idx += 1
elif tree_data[idx] == ',':
tokens.append(self.COMMA)
idx += 1
elif tree_data[idx] == '[':
# annotation
idx2 = tree_data.find(']', idx + 1)
rawstr = tree_data[idx + 1:idx2]
annotation = {}
for kv in rawstr.split(','):
k, v = kv.split("=", 1)
annotation[k] = v
obj = {
'type': self.ANNOTATION,
'annotation': annotation,
}
idx = idx2 + 1
tokens.append(obj)
elif tree_data[idx] == ':':
match = self.branch_re.search(tree_data, idx + 1)
assert (match is not None)
obj = {
'type': self.BRANCH,
'branch': float(tree_data[match.start():match.end()]),
}
idx = match.end()
tokens.append(obj)
else:
match = self.taxa_re.search(tree_data, idx)
assert (match is not None)
taxa = tree_data[match.start():match.end()]
obj = {
'type': self.NODE,
'taxa': taxa,
}
idx = match.end()
tokens.append(obj)
return tokens
def _parse(self, tokens):
count = 0
root = Node(_id=count)
count += 1
node = root
for token in tokens:
if token == self.START:
node2 = Node(_id=count)
count += 1
node.left = node2
node2.parent = node
node = node2
elif token == self.END:
node = node.parent
elif token == self.COMMA:
node2 = Node(_id=count)
count += 1
node.parent.right = node2
node2.parent = node.parent
node = node2
elif token['type'] == self.ANNOTATION:
node.annotation = token['annotation']
elif token['type'] == self.BRANCH:
node.branch = token['branch']
elif token['type'] == self.NODE:
node.name = token['taxa']
return root
#print(samplerAC)
t = Tree("((A, B)Internal_1:0.7, (C, D)Internal_2:0.5)root:1.3;", format=1)
t.add_features(size=4)
print t.get_ascii(attributes=["name", "dist", "size"])
#tree = Phylo.parse("/Users/patricioburchard/Downloads/Particiones_grupos_de_especies/part1.nex.con.tre", "nexus").next()
#tree = Phylo.read("/Users/patricioburchard/Downloads/Cercosaura_FinalPAUP.tre", "nexus")
#tree.rooted = True
#Phylo.draw(tree)
#infile = open('/Users/patricioburchard/Downloads/Particiones_grupos_de_especies/part1.nex.run1.p', 'r')
#t.show()
n = NexusReader(
'/Users/patricioburchard/Downloads/Particiones_grupos_de_especies/part1.nex.con.tre'
)
n.read_file(
'/Users/patricioburchard/Downloads/Particiones_grupos_de_especies/part1.nex.con.tre'
)
print(n.blocks)
#print(sorted(n.data.taxa))
#print(n.trees.ntrees[0])
for tree in n.trees:
print(tree)
#tree1 = dendropy.Tree.get_from_string(tree,"nexus")
import dendropy
#from dendropy import Tree
#from dendropy import TreeList
x = dendropy.Tree()
tree_list1 = dendropy.TreeList()
tree_list1.read_from_path(
"/Users/patricioburchard/Downloads/Particiones_grupos_de_especies/part1.nex.con.tre",
