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| author | zsloan | 2021-08-23 19:05:10 +0000 |
|---|---|---|
| committer | zsloan | 2021-08-23 19:05:10 +0000 |
| commit | 654b35c2050e89f9ba533a3713d40465cf6fcd47 (patch) | |
| tree | 29b1fcc769661e95d2786518a10e581020a0111a | |
| parent | 0bbe9072566397942a6db034cb11203bcb43b78f (diff) | |
| download | genenetwork2-654b35c2050e89f9ba533a3713d40465cf6fcd47.tar.gz | |
Fix get_perm_strata to usethe Ids for case attributes instead of names + allow perm_strata to be passed to the template
| -rw-r--r-- | wqflask/wqflask/marker_regression/run_mapping.py | 12 |
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: |