diff options
| -rw-r--r-- | wqflask/wqflask/marker_regression/gemma_mapping.py | 6 |
1 files changed, 0 insertions, 6 deletions
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index c4bcef8b..7a3d0312 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -148,8 +148,6 @@ def gen_covariates_file(this_dataset, covariates, samples): trait_ob = create_trait(dataset=dataset_ob, name=trait_name, cellid=None) - - #trait_samples = this_dataset.group.all_samples_ordered() this_dataset.group.get_samplelist() trait_samples = this_dataset.group.samplelist trait_sample_data = trait_ob.data @@ -184,10 +182,8 @@ def parse_loco_output(this_dataset, gwa_output_filename, loco="True"): marker_obs = [] previous_chr = 0 - no_results = False for this_file in output_filelist: if not os.path.isfile(this_file): - no_results = True break with open(this_file) as output_file: for line in output_file: @@ -212,10 +208,8 @@ def parse_loco_output(this_dataset, gwa_output_filename, loco="True"): marker['additive'] = float(line.split("\t")[7]) if math.isnan(marker['p_value']) or (marker['p_value'] <= 0): marker['lod_score'] = 0 - #marker['lrs_value'] = 0 else: marker['lod_score'] = -math.log10(marker['p_value']) - #marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61 marker_obs.append(marker) included_markers.append(line.split("\t")[1]) |