1 files changed, 44 insertions, 0 deletions
diff --git a/gn3/api/rqtl.py b/gn3/api/rqtl.py
new file mode 100644
index 0000000..de620f7
--- /dev/null
+++ b/gn3/api/rqtl.py
@@ -0,0 +1,44 @@
+"""Endpoints for running the rqtl cmd"""
+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"])
+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"]
+    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)
+
+    results = 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)