diff options
| -rw-r--r-- | gn3/api/rqtl.py | 20 |
1 files changed, 19 insertions, 1 deletions
diff --git a/gn3/api/rqtl.py b/gn3/api/rqtl.py index 8dd4bb7..82cf34f 100644 --- a/gn3/api/rqtl.py +++ b/gn3/api/rqtl.py @@ -2,8 +2,12 @@ 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.computations.gemma import do_paths_exist + rqtl = Blueprint("rqtl", __name__) @rqtl.route("/compute", methods=["POST"]) @@ -16,4 +20,18 @@ def compute(): if not do_paths_exist([genofile, phenofile]): raise FileNotFoundError - return current_app.config.get("RQTL_WRAPPER_CMD") \ No newline at end of file + kwarg_list = ["addcovar", "model", "method", "interval", "nperm", "scale", "control_marker"] + + rqtl_kwargs = {"geno": genofile, "pheno": phenofile} + for kwarg in kwarg_list: + if kwarg in request.form: + rqtl_kwargs[kwarg] = request.form[kwarg] + + results = generate_rqtl_cmd( + rqtl_wrapper_cmd = current_app.config.get("RQTL_WRAPPER_CMD"), + output_dir = current_app.config.get('TMPDIR'), + rqtl_wrapper_kwargs = rqtl_kwargs + ) + + return jsonify(results) + |