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)
