diff options
| -rwxr-xr-x | wqflask/wqflask/interval_mapping/interval_mapping.py | 29 |
1 files changed, 0 insertions, 29 deletions
diff --git a/wqflask/wqflask/interval_mapping/interval_mapping.py b/wqflask/wqflask/interval_mapping/interval_mapping.py index 5511826a..4b4b7f73 100755 --- a/wqflask/wqflask/interval_mapping/interval_mapping.py +++ b/wqflask/wqflask/interval_mapping/interval_mapping.py @@ -24,9 +24,6 @@ from base import data_set from base import species from base import webqtlConfig from utility import webqtlUtil -from wqflask.my_pylmm.data import prep_data -from wqflask.my_pylmm.pyLMM import lmm -from wqflask.my_pylmm.pyLMM import input from utility import helper_functions from utility import Plot, Bunch from utility import temp_data @@ -223,32 +220,6 @@ class IntervalMapping(object): "cM":reaper_locus.cM, "name":reaper_locus.name, "additive":qtl.additive} self.qtl_results.append(qtl) - def gen_pylmm_results(self, tempdata): - print("USING PYLMM") - self.dataset.group.get_markers() - - pheno_vector = np.array([val == "x" and np.nan or float(val) for val in self.vals]) - if self.dataset.group.species == "human": - p_values, t_stats = self.gen_human_results(pheno_vector, tempdata) - else: - genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers] - - no_val_samples = self.identify_empty_samples() - trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples) - - genotype_matrix = np.array(trimmed_genotype_data).T - - t_stats, p_values = lmm.run( - pheno_vector, - genotype_matrix, - restricted_max_likelihood=True, - refit=False, - temp_data=tempdata - ) - - print("p_values:", p_values) - self.dataset.group.markers.add_pvalues(p_values) - self.qtl_results = self.dataset.group.markers.markers def gen_qtl_results_2(self, tempdata): """Generates qtl results for plotting interval map""" |