diff options
Diffstat (limited to 'wqflask/wqflask/api/mapping.py')
| -rw-r--r-- | wqflask/wqflask/api/mapping.py | 15 |
1 files changed, 10 insertions, 5 deletions
diff --git a/wqflask/wqflask/api/mapping.py b/wqflask/wqflask/api/mapping.py index 662090d5..c22b44a9 100644 --- a/wqflask/wqflask/api/mapping.py +++ b/wqflask/wqflask/api/mapping.py @@ -37,20 +37,25 @@ def do_mapping_for_api(start_vars): mapping_params = initialize_parameters(start_vars, dataset, this_trait) - covariates = "" # ZS: It seems to take an empty string as default. This should probably be changed. + # ZS: It seems to take an empty string as default. This should probably be changed. + covariates = "" if mapping_params['mapping_method'] == "gemma": header_row = ["name", "chr", "Mb", "lod_score", "p_value"] - if mapping_params['use_loco'] == "True": # ZS: gemma_mapping returns both results and the filename for LOCO, so need to only grab the former for api - result_markers = gemma_mapping.run_gemma(this_trait, dataset, samples, vals, covariates, mapping_params['use_loco'], mapping_params['maf'])[0] + # ZS: gemma_mapping returns both results and the filename for LOCO, so need to only grab the former for api + if mapping_params['use_loco'] == "True": + result_markers = gemma_mapping.run_gemma( + this_trait, dataset, samples, vals, covariates, mapping_params['use_loco'], mapping_params['maf'])[0] else: - result_markers = gemma_mapping.run_gemma(this_trait, dataset, samples, vals, covariates, mapping_params['use_loco'], mapping_params['maf']) + result_markers = gemma_mapping.run_gemma( + this_trait, dataset, samples, vals, covariates, mapping_params['use_loco'], mapping_params['maf']) elif mapping_params['mapping_method'] == "rqtl": header_row = ["name", "chr", "cM", "lod_score"] if mapping_params['num_perm'] > 0: _sperm_output, _suggestive, _significant, result_markers = rqtl_mapping.run_rqtl_geno(vals, dataset, mapping_params['rqtl_method'], mapping_params['rqtl_model'], mapping_params['perm_check'], mapping_params['num_perm'], - mapping_params['do_control'], mapping_params['control_marker'], + mapping_params['do_control'], mapping_params[ + 'control_marker'], mapping_params['manhattan_plot'], mapping_params['pair_scan']) else: result_markers = rqtl_mapping.run_rqtl_geno(vals, dataset, mapping_params['rqtl_method'], mapping_params['rqtl_model'], |