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authorzsloan2021-05-25 20:27:05 +0000
committerzsloan2021-05-25 20:27:05 +0000
commitd3a4146fd38fc1d372091cecadfcf7c8fb377f3b (patch)
treef89a04f0aac8d423495cf4340e46e983a1c2fd05 /gn3/api
parent578a5770c4280c50dc43753429310a43cb6d7e68 (diff)
downloadgenenetwork3-d3a4146fd38fc1d372091cecadfcf7c8fb377f3b.tar.gz
Include code that processes rqtl output files and returns actual results instead of just the output filename
Diffstat (limited to 'gn3/api')
-rw-r--r--gn3/api/rqtl.py16
1 files changed, 13 insertions, 3 deletions
diff --git a/gn3/api/rqtl.py b/gn3/api/rqtl.py
index de620f7..0194b6f 100644
--- a/gn3/api/rqtl.py
+++ b/gn3/api/rqtl.py
@@ -1,10 +1,13 @@
"""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
+from gn3.commands import run_cmd
+from gn3.computations.rqtl import generate_rqtl_cmd, process_rqtl_output, process_perm_output
from gn3.computations.gemma import do_paths_exist
rqtl = Blueprint("rqtl", __name__)
@@ -35,10 +38,17 @@ run the rqtl_wrapper script and return the results as JSON
if kwarg in boolean_kwargs:
rqtl_bool_kwargs.append(kwarg)
- results = generate_rqtl_cmd(
+ rqtl_cmd = generate_rqtl_cmd(
rqtl_wrapper_cmd=current_app.config.get("RQTL_WRAPPER_CMD"),
rqtl_wrapper_kwargs=rqtl_kwargs,
rqtl_wrapper_bool_kwargs=boolean_kwargs
)
- return jsonify(results)
+ os.system(rqtl_cmd.get('rqtl_cmd'))
+
+ rqtl_output = {}
+ rqtl_output['results'] = process_rqtl_output(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)