diff options
Diffstat (limited to 'gn3/api/rqtl.py')
| -rw-r--r-- | gn3/api/rqtl.py | 11 |
1 files changed, 7 insertions, 4 deletions
diff --git a/gn3/api/rqtl.py b/gn3/api/rqtl.py index 0194b6f..38f4c1e 100644 --- a/gn3/api/rqtl.py +++ b/gn3/api/rqtl.py @@ -26,7 +26,7 @@ run the rqtl_wrapper script and return the results as JSON # 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"] + boolean_kwargs = ["addcovar", "interval", "pstrata"] all_kwargs = kwargs + boolean_kwargs rqtl_kwargs = {"geno": genofile, "pheno": phenofile} @@ -41,12 +41,15 @@ run the rqtl_wrapper script and return the results as JSON 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 + rqtl_wrapper_bool_kwargs=rqtl_bool_kwargs ) - os.system(rqtl_cmd.get('rqtl_cmd')) - 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')) |