From 5e106bad6e59d3a13be0b79715785948a3ff581a Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sat, 10 Sep 2016 11:57:55 +0200
Subject: Comment

---
 wqflask/maintenance/gen_select_dataset.py              |  2 +-
 wqflask/wqflask/marker_regression/marker_regression.py | 16 ++++++++--------
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index 5c25c15b..f2f0830f 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -3,7 +3,7 @@
 Writes out data as /static/new/javascript/dataset_menu_structure.json
 It needs to be run manually when database has been changed. Run it as
 
-    python gen_select_dataset.py
+  ./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py
 
 """
 
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index f3b018b8..a1065adc 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -57,7 +57,7 @@ class MarkerRegression(object):
 
         all_samples_ordered = self.dataset.group.all_samples_ordered()
         primary_sample_names = list(all_samples_ordered)
-        
+
         for sample in self.dataset.group.samplelist:
             in_trait_data = False
             for item in self.this_trait.data:
@@ -241,9 +241,9 @@ class MarkerRegression(object):
                         highest_chr = marker['chr']
                     if ('lod_score' in marker.keys()) or ('lrs_value' in marker.keys()):
                         self.qtl_results.append(marker)
-       
+
             self.trimmed_markers = trim_markers_for_table(results)
-			
+
             self.json_data['chr'] = []
             self.json_data['pos'] = []
             self.json_data['lod.hk'] = []
@@ -560,7 +560,7 @@ class MarkerRegression(object):
 
 
     def gen_pheno_txt_file_plink(self, pheno_filename = ''):
-        ped_sample_list = self.get_samples_from_ped_file()	
+        ped_sample_list = self.get_samples_from_ped_file()
         output_file = open("%s%s.txt" % (TMPDIR, pheno_filename), "wb")
         header = 'FID\tIID\t%s\n' % self.this_trait.name
         output_file.write(header)
@@ -595,7 +595,7 @@ class MarkerRegression(object):
         output_file.close()
 
     def gen_pheno_txt_file_rqtl(self, pheno_filename = ''):
-        ped_sample_list = self.get_samples_from_ped_file()	
+        ped_sample_list = self.get_samples_from_ped_file()
         output_file = open("%s%s.txt" % (TMPDIR, pheno_filename), "wb")
         header = 'FID\tIID\t%s\n' % self.this_trait.name
         output_file.write(header)
@@ -653,7 +653,7 @@ class MarkerRegression(object):
             genotype = genotype.addinterval()
 
         samples, values, variances, sample_aliases = self.this_trait.export_informative()
-        
+
         trimmed_samples = []
         trimmed_values = []
         for i in range(0, len(samples)):
@@ -818,7 +818,7 @@ class MarkerRegression(object):
         """Runs permutations and gets significant and suggestive LOD scores"""
 
         top_lod_scores = []
-	
+
         #print("self.num_perm:", self.num_perm)
 
         for permutation in range(self.num_perm):
@@ -1084,7 +1084,7 @@ def create_snp_iterator_file(group):
 
 def trim_markers_for_table(markers):
     num_markers = len(markers)
-	
+
     if 'lod_score' in markers[0].keys():
         sorted_markers = sorted(markers, key=lambda k: k['lod_score'], reverse=True)
     else:
-- 
cgit v1.2.3