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
|
"""Endpoints for running the rqtl cmd"""
import os
from flask import Blueprint
from flask import current_app
from flask import jsonify
from flask import request
from gn3.computations.rqtl import generate_rqtl_cmd, process_rqtl_mapping, process_rqtl_pairscan, process_perm_output
from gn3.computations.gemma import do_paths_exist
rqtl = Blueprint("rqtl", __name__)
@rqtl.route("/compute", methods=["POST"])
def compute():
"""Given at least a geno_file and pheno_file, generate and
run the rqtl_wrapper script and return the results as JSON
"""
genofile = request.form['geno_file']
phenofile = request.form['pheno_file']
if not do_paths_exist([genofile, phenofile]):
raise FileNotFoundError
# Split kwargs by those with values and boolean ones that just convert to True/False
kwargs = ["covarstruct", "model", "method", "nperm", "scale", "control_marker"]
boolean_kwargs = ["addcovar", "interval", "pstrata", "pairscan"]
all_kwargs = kwargs + boolean_kwargs
rqtl_kwargs = {"geno": genofile, "pheno": phenofile}
rqtl_bool_kwargs = []
for kwarg in all_kwargs:
if kwarg in request.form:
if kwarg in kwargs:
rqtl_kwargs[kwarg] = request.form[kwarg]
if kwarg in boolean_kwargs:
rqtl_bool_kwargs.append(kwarg)
rqtl_cmd = generate_rqtl_cmd(
rqtl_wrapper_cmd=current_app.config.get("RQTL_WRAPPER_CMD"),
rqtl_wrapper_kwargs=rqtl_kwargs,
rqtl_wrapper_bool_kwargs=rqtl_bool_kwargs
)
rqtl_output = {}
if not os.path.isfile(os.path.join(current_app.config.get("TMPDIR"),
"output", rqtl_cmd.get('output_file'))):
os.system(rqtl_cmd.get('rqtl_cmd'))
if "pairscan" in boolean_kwargs:
rqtl_output['results'] = process_rqtl_pairscan(rqtl_cmd.get('output_file'), genofile)
else:
rqtl_output['results'] = process_rqtl_mapping(rqtl_cmd.get('output_file'))
if int(rqtl_kwargs['nperm']) > 0:
rqtl_output['perm_results'], rqtl_output['suggestive'], rqtl_output['significant'] = \
process_perm_output(rqtl_cmd.get('output_file'))
return jsonify(rqtl_output)
|
