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
|
"""Run the 'sample' correlations.
Converts code in
https://github.com/genenetwork/genenetwork2/blob/a08d91a234f700043d1d31164c7e2bacda4729da/wqflask/wqflask/correlation/correlation_gn3_api.py#L211-L216
into a script that can be run as an external process."""
import sys
import pickle
from argparse import ArgumentParser
from gn3.computations.correlations import compute_all_sample_correlation
from scripts.argparse_actions import FileCheck
# compute_all_sample_correlation(
# corr_method=method, this_trait=this_trait_data, target_dataset=target_dataset_data)
if __name__ == "__main__":
def cli_args():
"Process the command-line arguments."
parser = ArgumentParser(prog="sample_correlations")
parser.add_argument(
"corrmethod", help="The correlation method to use.", type=str,
choices=("pearson", "spearman", "bicor"))
parser.add_argument(
"traitfile", help="Path to file with pickled trait.",
type=str, action=FileCheck)
parser.add_argument(
"targetdataset", type=str, action=FileCheck,
help="Path to file with pickled target dataset traits.")
parser.add_argument(
"destfile", type=str,
help=("Path to file with pickled results of computing the "
"correlations."))
args = parser.parse_args()
return args
def main():
"CLI entry-point function"
args = cli_args()
with open(args.traitfile, "rb") as traitfile:
with open(args.targetdataset, "rb") as targetdataset:
corrs = compute_all_sample_correlation(
corr_method=args.corrmethod,
this_trait=pickle.load(traitfile),
target_dataset=pickle.load(targetdataset))
with open(args.destfile, "wb") as dest:
pickle.dump(corrs, dest)
return 0
sys.exit(main())
|
