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authorzsloan2021-08-23 19:05:10 +0000
committerzsloan2021-08-23 19:05:10 +0000
commit654b35c2050e89f9ba533a3713d40465cf6fcd47 (patch)
tree29b1fcc769661e95d2786518a10e581020a0111a /wqflask
parent0bbe9072566397942a6db034cb11203bcb43b78f (diff)
downloadgenenetwork2-654b35c2050e89f9ba533a3713d40465cf6fcd47.tar.gz
Fix get_perm_strata to usethe Ids for case attributes instead of names + allow perm_strata to be passed to the template
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/wqflask/marker_regression/run_mapping.py12
1 files changed, 6 insertions, 6 deletions
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index f601201b..ebad7d36 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -220,7 +220,7 @@ class RunMapping:
elif self.mapping_method == "rqtl_plink":
results = self.run_rqtl_plink()
elif self.mapping_method == "rqtl_geno":
- perm_strata = []
+ self.perm_strata = []
if "perm_strata" in start_vars and "categorical_vars" in start_vars:
self.categorical_vars = start_vars["categorical_vars"].split(
",")
@@ -229,7 +229,7 @@ class RunMapping:
sample_names=self.samples,
this_trait=self.this_trait)
- perm_strata = get_perm_strata(
+ self.perm_strata = get_perm_strata(
self.this_trait, primary_samples, self.categorical_vars, self.samples)
self.score_type = "LOD"
self.control_marker = start_vars['control_marker']
@@ -243,10 +243,10 @@ class RunMapping:
# self.pair_scan = True
if self.permCheck and self.num_perm > 0:
self.perm_output, self.suggestive, self.significant, results = rqtl_mapping.run_rqtl(
- self.this_trait.name, self.vals, self.samples, self.dataset, self.mapping_scale, self.model, self.method, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.covariates)
+ self.this_trait.name, self.vals, self.samples, self.dataset, self.mapping_scale, self.model, self.method, self.num_perm, self.perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.covariates)
else:
results = rqtl_mapping.run_rqtl(self.this_trait.name, self.vals, self.samples, self.dataset, self.mapping_scale, self.model, self.method,
- self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.covariates)
+ self.num_perm, self.perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.covariates)
elif self.mapping_method == "reaper":
if "startMb" in start_vars: # ZS: Check if first time page loaded, so it can default to ON
if "additiveCheck" in start_vars:
@@ -765,9 +765,9 @@ def get_perm_strata(this_trait, sample_list, categorical_vars, used_samples):
if sample in list(sample_list.sample_attribute_values.keys()):
combined_string = ""
for var in categorical_vars:
- if var.lower() in sample_list.sample_attribute_values[sample]:
+ if var in sample_list.sample_attribute_values[sample]:
combined_string += str(
- sample_list.sample_attribute_values[sample][var.lower()])
+ sample_list.sample_attribute_values[sample][var])
else:
combined_string += "NA"
else: