def main_regex (opts):
print "in main regex"
rdr = NewickReader ({'node_annotations': True})
in_tree = rdr.read (opts.in_tree_path)
match_regex = re.compile (opts.match_pat)
for t in in_tree.iter_tip_nodes():
t.title = match_regex.sub (opts.replace_pat, t.title)
wrtr = NewickWriter ()
wrtr._dist_format = opts.distance_format[0]
wrtr.write (in_tree, opts.out_tree_path)
def main_regex(opts):
print "in main regex"
rdr = NewickReader({'node_annotations': True})
in_tree = rdr.read(opts.in_tree_path)
match_regex = re.compile(opts.match_pat)
for t in in_tree.iter_tip_nodes():
t.title = match_regex.sub(opts.replace_pat, t.title)
wrtr = NewickWriter()
wrtr._dist_format = opts.distance_format[0]
wrtr.write(in_tree, opts.out_tree_path)
def main_map (opts):
from csv import DictReader
csv_reader = DictReader (opts.in_csv_path)
name_map = {}
for r in csv_reader:
name_map[r[opts.in_col]] = r[opts.out_col]
# now rewrite the tree
rdr = NewickReader ({'node_annotations': True})
in_tree = rdr.read (opts.in_tree_path)
for t in in_tree.iter_tip_nodes():
t.title = name_map.get(t.title, t.title)
wrtr = NewickWriter ()
wrtr._dist_format = opts.distance_format[0]
wrtr.write (in_tree, opts.out_tree_path)
def main_map(opts):
from csv import DictReader
csv_reader = DictReader(opts.in_csv_path)
name_map = {}
for r in csv_reader:
name_map[r[opts.in_col]] = r[opts.out_col]
# now rewrite the tree
rdr = NewickReader({'node_annotations': True})
in_tree = rdr.read(opts.in_tree_path)
for t in in_tree.iter_tip_nodes():
t.title = name_map.get(t.title, t.title)
wrtr = NewickWriter()
wrtr._dist_format = opts.distance_format[0]
wrtr.write(in_tree, opts.out_tree_path)
class NexusReader (io.BaseReader):
def __init__ (self, dialect={}, tree_kls=Tree):
io.BaseReader.__init__ (self, dialect=dialect)
self._newick_rdr = NewickReader (dialect=self.dialect, tree_kls=Tree)
def _read (self, src):
"""
Read the passed tree and return a Phylotree structure.
:Params:
src
An open file or file-like object.
:Returns:
A phylotree.
"""
## Preconditions & preparation:
## Main:
file_str = src.read()
m = _TREE_BLK_REGEX.search (file_str)
assert (m), "can't find tree block"
blk_str = m.group(1)
m = _TRANS_TABLE_REGEX.search (blk_str)
if m:
trans_str = m.group(1)
lines = trans_str.split(',')
prs = [x.strip().split(' ', 1) for x in lines]
table = {}
for p in prs:
k = p[0]
v = p[1]
if v.startswith('\''):
v = v[1:-1]
table[k] = v
else:
table = {}
m = FIRST_TREE_REGEX.search (blk_str)
assert (m), "can't find tree entry in block"
tree_line = m.group(1)
m = TREE_STR_REGEX.search (tree_line)
assert (m), "can't find newick tree in line"
tree_src = cStringIO.StringIO (m.group(1))
t = self._newick_rdr.read (tree_src)
if table:
for n in t.iter_nodes():
new_name = table.get(n.title, None)
if new_name:
n.title = new_name
return t
def __init__ (self, dialect={}, tree_kls=Tree):
io.BaseReader.__init__ (self, dialect=dialect)
self._newick_rdr = NewickReader (dialect=self.dialect, tree_kls=Tree)
