1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
|
import click
from bp import parse_jplace, insert_fully_resolved
try:
from bp.GPL import insert_multifurcating
except:
insert_multifurcating = None
@click.group()
def cli():
pass
@cli.command()
@click.option('--placements', type=click.Path(exists=True),
required=True, help='jplace formatted data')
@click.option('--output', type=click.Path(exists=False),
required=True, help='Where to write the resulting newick')
@click.option('--method',
type=click.Choice(['fully-resolved', 'multifurcating']),
required=True, help='Whether to fully resolve or multifurcate')
def placement(placements, output, method):
if method == 'fully-resolved':
f = insert_fully_resolved
elif method == 'multifurcating':
if insert_multifurcating is None:
raise ValueError("Please install with 'pip install iow-gpl'")
f = insert_multifurcating
else:
raise ValueError("Unknown method: %s" % method)
placement_df, tree = parse_jplace(open(placements).read())
sktree = f(placement_df, tree)
sktree.write(output)
if __name__ == '__main__':
cli()
|
