diff options
| -rw-r--r-- | wqflask/wqflask/marker_regression/rqtl_mapping.py | 7 |
1 files changed, 2 insertions, 5 deletions
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py index 1dca1b1b..34b10fc5 100644 --- a/wqflask/wqflask/marker_regression/rqtl_mapping.py +++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py @@ -12,14 +12,11 @@ import numpy as np from base.webqtlConfig import TMPDIR from base.trait import create_trait -from utility.tools import locate +from utility.tools import locate, GN3_LOCAL_URL import utility.logger logger = utility.logger.getLogger(__name__) -GN3_RQTL_URL = "http://localhost:8086/api/rqtl/compute" -GN3_TMP_PATH = "/export/local/home/zas1024/genenetwork3/tmp" - def run_rqtl(trait_name, vals, samples, dataset, mapping_scale, model, method, num_perm, perm_strata_list, do_control, control_marker, manhattan_plot, cofactors): """Run R/qtl by making a request to the GN3 endpoint and reading in the output file(s)""" @@ -49,7 +46,7 @@ def run_rqtl(trait_name, vals, samples, dataset, mapping_scale, model, method, n if perm_strata_list: post_data["pstrata"] = True - rqtl_output = requests.post(GN3_RQTL_URL, data=post_data).json() + rqtl_output = requests.post(GN3_LOCAL_URL + "api/rqtl/compute", data=post_data).json() if num_perm > 0: return rqtl_output['perm_results'], rqtl_output['suggestive'], rqtl_output['significant'], rqtl_output['results'] else: |