def __load_tree_txt__(self, fn):
tree = Phylo.BaseTree.Tree()
try:
rows = [
l.decode('utf-8').rstrip().split("\t")[0]
for l in open(fn, 'rb')
]
except IOError:
raise IOError()
clades = [r.split(self.lev_sep) for r in rows]
tree = BTree()
tree.root = BClade()
def add_clade_rec(father, txt_tree):
fl = set([t[0] for t in txt_tree])
father.clades = []
for c in fl:
nclade = BClade(branch_length=1.0, name=c)
father.clades.append(nclade)
children = [
t[1:] for t in txt_tree if len(t) > 1 and t[0] == c
]
if children:
add_clade_rec(nclade, children)
add_clade_rec(tree.root, clades)
self.ignore_branch_len = 1
return tree.as_phyloxml()
def __load_tree_txt__( self, fn ):
tree = Phylo.BaseTree.Tree()
try:
rows = [l.decode('utf-8').rstrip().split("\t")[0] for l in
open(fn, 'rb')]
except IOError:
raise IOError()
clades = [r.split(lev_sep) for r in rows]
tree = BTree()
tree.root = BClade()
def add_clade_rec( father, txt_tree ):
fl = set([t[0] for t in txt_tree])
father.clades = []
for c in fl:
nclade = BClade( branch_length = 1.0,
name = c )
father.clades.append( nclade )
children = [t[1:] for t in txt_tree if len(t)>1 and t[0] == c]
if children:
add_clade_rec( nclade, children )
add_clade_rec( tree.root, clades )
self.ignore_branch_len = 1
return tree.as_phyloxml()
def exp_newick(inp, labels, outfile, tree_format='phyloxml'):
n_leaves = int(inp[-1][-1])
from Bio import Phylo
import collections
from Bio.Phylo.BaseTree import Tree as BTree
from Bio.Phylo.BaseTree import Clade as BClade
tree = BTree()
tree.root = BClade()
subclades = {}
sb_cbl = {}
for i, (fr, to, bl, nsub) in enumerate(inp):
if fr < n_leaves:
fr_c = BClade(branch_length=-1.0, name=labels[int(fr)])
subclades[fr] = fr_c
sb_cbl[fr] = bl
if to < n_leaves:
to_c = BClade(branch_length=-1.0, name=labels[int(to)])
subclades[to] = to_c
sb_cbl[to] = bl
for i, (fr, to, bl, nsub) in enumerate(inp):
fr_c = subclades[fr]
to_c = subclades[to]
cur_c = BClade(branch_length=bl)
cur_c.clades.append(fr_c)
cur_c.clades.append(to_c)
subclades[i + n_leaves] = cur_c
def reset_rec(clade, fath_bl):
if clade.branch_length < 0:
clade.branch_length = fath_bl
return
for c in clade.clades:
reset_rec(c, clade.branch_length)
clade.branch_length = fath_bl - clade.branch_length
tree.root = cur_c
reset_rec(tree.root, 0.0)
tree.root.branch_length = 0.0
Phylo.write(tree, outfile, tree_format)