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-rw-r--r--gn3/api/rqtl.py16
1 files changed, 12 insertions, 4 deletions
diff --git a/gn3/api/rqtl.py b/gn3/api/rqtl.py
index 7756310..de620f7 100644
--- a/gn3/api/rqtl.py
+++ b/gn3/api/rqtl.py
@@ -21,16 +21,24 @@ run the rqtl_wrapper script and return the results as JSON
if not do_paths_exist([genofile, phenofile]):
raise FileNotFoundError
- kwarg_list = ["addcovar", "model", "method", "interval", "nperm", "scale", "control_marker"]
+ # 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}
- for kwarg in kwarg_list:
+ rqtl_bool_kwargs = []
+ for kwarg in all_kwargs:
if kwarg in request.form:
- rqtl_kwargs[kwarg] = request.form[kwarg]
+ 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_kwargs=rqtl_kwargs,
+ rqtl_wrapper_bool_kwargs=boolean_kwargs
)
return jsonify(results)