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| author | BonfaceKilz | 2021-02-03 17:40:06 +0300 |
|---|---|---|
| committer | BonfaceKilz | 2021-02-05 08:31:38 +0300 |
| commit | 56016aaec031149b2525e01429372619aaf4095d (patch) | |
| tree | f4c02f23f4548a17d38e2ba1c86080ecd08b9bfb | |
| parent | 92760af93f4eaeae1852be31e38e11693698e3f2 (diff) | |
| download | genenetwork2-56016aaec031149b2525e01429372619aaf4095d.tar.gz | |
Remove commented out code and unused variables
| -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]) |