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-rw-r--r--wqflask/maintenance/gen_select_dataset.py2
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression.py16
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: