diff options
| -rw-r--r-- | wqflask/maintenance/gen_select_dataset.py | 2 | ||||
| -rw-r--r-- | 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: |