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authorzsloan2021-06-18 17:33:09 -0500
committerGitHub2021-06-18 17:33:09 -0500
commitd653a635d0efd2291754c18f51d31f91a1c0a25c (patch)
tree309ea800da204f721e92ebc1c725144eab939d0f /gn3/api
parentc553b52e140de1d7e5ed49f07bae2f4a120266f8 (diff)
parentf7becfa11ca857104ecc1b668b4bd3d0a721083c (diff)
downloadgenenetwork3-d653a635d0efd2291754c18f51d31f91a1c0a25c.tar.gz
Merge pull request #13 from zsloan/feature/add_rqtl_endpoints
Feature/add rqtl endpoints
Diffstat (limited to 'gn3/api')
-rw-r--r--gn3/api/rqtl.py58
1 files changed, 58 insertions, 0 deletions
diff --git a/gn3/api/rqtl.py b/gn3/api/rqtl.py
new file mode 100644
index 0000000..ebb746c
--- /dev/null
+++ b/gn3/api/rqtl.py
@@ -0,0 +1,58 @@
+"""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_output, 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 = ["model", "method", "nperm", "scale", "control_marker"]
+ boolean_kwargs = ["addcovar", "interval", "pstrata"]
+ 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'))
+
+ rqtl_output['results'] = process_rqtl_output(rqtl_cmd.get('output_file'))
+
+ 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)