Fixed issue that caused some GEMMA results to appear incorrectly

1 files changed, 6 insertions, 7 deletions

diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 68920130..54cde3c6 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -3,7 +3,7 @@ import os, math, string, random, json
 from base import webqtlConfig
 from base.trait import GeneralTrait
 from base.data_set import create_dataset
-from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND, TEMPDIR, assert_bin, assert_file
+from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND, TEMPDIR
 
 import utility.logger
 logger = utility.logger.getLogger(__name__ )
@@ -11,7 +11,6 @@ logger = utility.logger.getLogger(__name__ )
 def run_gemma(this_dataset, samples, vals, covariates, method, use_loco):
     """Generates p-values for each marker using GEMMA"""
 
-    assert_bin(GEMMA_COMMAND);
     if this_dataset.group.genofile != None:
         genofile_name = this_dataset.group.genofile[:-5]
     else:
@@ -193,7 +192,7 @@ def parse_gemma_output(genofile_name):
                 # if marker['chr'] != previous_chr:
                     # previous_chr = marker['chr']
                 marker['Mb'] = float(line.split("\t")[2]) / 1000000
-                marker['p_value'] = float(line.split("\t")[10])
+                marker['p_value'] = float(line.split("\t")[11])
                 if math.isnan(marker['p_value']) or (marker['p_value'] <= 0):
                     marker['lod_score'] = 0
                     #marker['lrs_value'] = 0
@@ -203,7 +202,7 @@ def parse_gemma_output(genofile_name):
                 marker_obs.append(marker)
 
                 included_markers.append(line.split("\t")[1])
-                p_values.append(float(line.split("\t")[10]))
+                p_values.append(float(line.split("\t")[11]))
 
     return marker_obs
 
@@ -241,7 +240,7 @@ def parse_loco_output(this_dataset, gwa_output_filename):
                     else:
                         marker['chr'] = line.split("\t")[0]
                     marker['Mb'] = float(line.split("\t")[2]) / 1000000
-                    marker['p_value'] = float(line.split("\t")[10])
+                    marker['p_value'] = float(line.split("\t")[11])
                     if math.isnan(marker['p_value']) or (marker['p_value'] <= 0):
                         marker['lod_score'] = 0
                         #marker['lrs_value'] = 0
@@ -251,6 +250,6 @@ def parse_loco_output(this_dataset, gwa_output_filename):
                     marker_obs.append(marker)
 
                     included_markers.append(line.split("\t")[1])
-                    p_values.append(float(line.split("\t")[10]))
+                    p_values.append(float(line.split("\t")[11]))
 
-    return marker_obs
+    return marker_obs
\ No newline at end of file