diff options
| -rw-r--r-- | wqflask/wqflask/api/mapping.py | 14 |
1 files changed, 7 insertions, 7 deletions
diff --git a/wqflask/wqflask/api/mapping.py b/wqflask/wqflask/api/mapping.py index 0a23457e..5eacc83a 100644 --- a/wqflask/wqflask/api/mapping.py +++ b/wqflask/wqflask/api/mapping.py @@ -19,7 +19,7 @@ def do_mapping_for_api(start_vars): mapping_params = initialize_parameters(start_vars, dataset, this_trait) genofile_samplelist = [] - if mapping_params['genofile']: + if mapping_params.get('genofile'): dataset.group.genofile = mapping_params['genofile'] genofile_samplelist = get_genofile_samplelist(dataset) @@ -50,7 +50,7 @@ def do_mapping_for_api(start_vars): if not in_trait_data: vals.append("x") - if mapping_params['transform'] == "qnorm": + if mapping_params.get('transform') == "qnorm": vals_minus_x = [float(val) for val in vals if val != "x"] qnorm_vals = normf(vals_minus_x) qnorm_vals_with_x = [] @@ -67,16 +67,16 @@ def do_mapping_for_api(start_vars): # It seems to take an empty string as default. This should probably be changed. covariates = "" - if mapping_params['mapping_method'] == "gemma": + if mapping_params.get('mapping_method') == "gemma": header_row = ["name", "chr", "Mb", "lod_score", "p_value"] # 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": + if mapping_params.get('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']) - elif mapping_params['mapping_method'] == "rqtl": + elif mapping_params.get('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(this_trait.name, vals, samples, dataset, None, "Mb", mapping_params['rqtl_model'], @@ -89,10 +89,10 @@ def do_mapping_for_api(start_vars): mapping_params['do_control'], mapping_params['control_marker'], mapping_params['manhattan_plot'], None) - if mapping_params['limit_to']: + if mapping_params.get('limit_to'): result_markers = result_markers[:mapping_params['limit_to']] - if mapping_params['format'] == "csv": + if mapping_params.get('format') == "csv": output_rows = [] output_rows.append(header_row) for marker in result_markers: |