-
Notifications
You must be signed in to change notification settings - Fork 4
/
poppipe_assign.py
96 lines (78 loc) · 3.25 KB
/
poppipe_assign.py
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
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
#!/usr/bin/env python
# vim: set fileencoding=<utf-8> :
import sys, os
import pandas as pd
import re
import subprocess
import tempfile
import yaml
# script outputs
combined_rfile = "combined_rfile.txt"
combined_clusters = "combined_clusters.csv"
combined_db = "combined_db.h5"
output_yaml = "config.yml"
# command line parsing
def get_options():
import argparse
parser = argparse.ArgumentParser(description='Update PopPIPE results with queries',
prog='poppipe_assign.py')
# input options
qGroup = parser.add_argument_group('poppunk_assign files')
qGroup.add_argument('--query', required=True, help='Argument given to --query')
qGroup.add_argument('--db', required=True, help='Argument given to --db')
qGroup.add_argument('--output', required=True, help='Argument given to --output')
smGroup = parser.add_argument_group('snakemake files')
smGroup.add_argument('--config', required=True, help='config.yml from snakemake')
other = parser.add_argument_group('Other options')
other.add_argument('--recalculate-random', default=False, action='store_true',
help='Recalculate random matches when joining databases')
return parser.parse_args()
# main code
if __name__ == "__main__":
# Get command line options
args = get_options()
if args.config == output_yaml:
sys.stderr.write("Output config file " + output_yaml + " exists\n")
output_yaml = tempfile.mkstemp(dir=".", prefix="config.", suffix=".yml")[1]
sys.stderr.write("Using " + output_yaml + " instead\n")
with open(args.config, 'r') as stream:
try:
config_in = yaml.safe_load(stream)
except yaml.YAMLError as exc:
print(exc)
sys.exit(1)
rfile = config_in['poppunk_rfile']
clusters = config_in['poppunk_clusters']
h5 = config_in['poppunk_h5']
# Join files
with open(combined_rfile, 'w') as rfile_out:
with open(rfile, 'r') as r1_in:
rfile_out.write(r1_in.read())
with open(args.query, 'r') as r2_in:
rfile_out.write(r2_in.read())
# Join clusters
ref_clusters = pd.read_table(clusters, sep=",",).set_index("Taxon")
query_clusters = pd.read_table(
args.output + "/" + os.path.basename(args.output) + "_clusters.csv",
sep=",",).set_index("Taxon")
ref_clusters = ref_clusters.append(query_clusters)
ref_clusters.to_csv(combined_clusters, sep=",")
# Join DBs
h5_re = re.compile(r"^(.+)\.h5$")
ref_prefix = re.match(h5_re, h5).group(1)
output_prefix = re.match(h5_re, combined_db).group(1)
query_prefix = args.output + "/" + os.path.basename(args.output)
join_cmd = "sketchlib join " + ref_prefix + " " + \
query_prefix + " -o " + \
output_prefix
subprocess.run(join_cmd, shell=True, check=True)
if args.recalculate_random:
subprocess.run("sketchlib add random " + \
output_prefix,
shell=True, check=True)
config_in['poppunk_rfile'] = combined_rfile
config_in['poppunk_clusters'] = combined_clusters
config_in['poppunk_h5'] = combined_db
with open(output_yaml, 'w') as stream:
output = yaml.dump(config_in, stream)
sys.exit(0)