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authorBonfaceKilz2021-02-03 17:40:06 +0300
committerBonfaceKilz2021-02-05 08:31:38 +0300
commit56016aaec031149b2525e01429372619aaf4095d (patch)
treef4c02f23f4548a17d38e2ba1c86080ecd08b9bfb /wqflask
parent92760af93f4eaeae1852be31e38e11693698e3f2 (diff)
downloadgenenetwork2-56016aaec031149b2525e01429372619aaf4095d.tar.gz
Remove commented out code and unused variables
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/wqflask/marker_regression/gemma_mapping.py6
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])