diff options
Diffstat (limited to 'wqflask/wqflask/api/mapping.py')
| -rw-r--r-- | wqflask/wqflask/api/mapping.py | 186 |
1 files changed, 0 insertions, 186 deletions
diff --git a/wqflask/wqflask/api/mapping.py b/wqflask/wqflask/api/mapping.py deleted file mode 100644 index 5eacc83a..00000000 --- a/wqflask/wqflask/api/mapping.py +++ /dev/null @@ -1,186 +0,0 @@ -from base import data_set -from base.trait import create_trait, retrieve_sample_data - -from wqflask.marker_regression import gemma_mapping, rqtl_mapping -from wqflask.show_trait.show_trait import normf - -def do_mapping_for_api(start_vars): - if ('db' not in start_vars) or ("trait_id" not in start_vars): - raise ValueError("Mapping: db and trait_id are not in start_vars") - - dataset = data_set.create_dataset(dataset_name=start_vars['db']) - dataset.group.get_markers() - this_trait = create_trait(dataset=dataset, name=start_vars['trait_id']) - this_trait = retrieve_sample_data(this_trait, dataset) - - samples = [] - vals = [] - - mapping_params = initialize_parameters(start_vars, dataset, this_trait) - - genofile_samplelist = [] - if mapping_params.get('genofile'): - dataset.group.genofile = mapping_params['genofile'] - genofile_samplelist = get_genofile_samplelist(dataset) - - if (len(genofile_samplelist) > 0): - samplelist = genofile_samplelist - for sample in samplelist: - in_trait_data = False - for item in this_trait.data: - if this_trait.data[item].name == sample: - value = str(this_trait.data[item].value) - samples.append(item) - vals.append(value) - in_trait_data = True - break - if not in_trait_data: - vals.append("x") - else: - samplelist = dataset.group.samplelist - for sample in samplelist: - in_trait_data = False - for item in this_trait.data: - if this_trait.data[item].name == sample: - value = str(this_trait.data[item].value) - samples.append(item) - vals.append(value) - in_trait_data = True - break - if not in_trait_data: - vals.append("x") - - 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 = [] - counter = 0 - for val in vals: - if val == "x": - qnorm_vals_with_x.append("x") - else: - qnorm_vals_with_x.append(qnorm_vals[counter]) - counter += 1 - - vals = qnorm_vals_with_x - - # It seems to take an empty string as default. This should probably be changed. - covariates = "" - - 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.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.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'], - mapping_params['rqtl_method'], mapping_params['num_perm'], None, - mapping_params['do_control'], mapping_params['control_marker'], - mapping_params['manhattan_plot'], None) - else: - result_markers = rqtl_mapping.run_rqtl(this_trait.name, vals, samples, dataset, None, "Mb", mapping_params['rqtl_model'], - mapping_params['rqtl_method'], mapping_params['num_perm'], None, - mapping_params['do_control'], mapping_params['control_marker'], - mapping_params['manhattan_plot'], None) - - if mapping_params.get('limit_to'): - result_markers = result_markers[:mapping_params['limit_to']] - - if mapping_params.get('format') == "csv": - output_rows = [] - output_rows.append(header_row) - for marker in result_markers: - this_row = [marker[header] for header in header_row] - output_rows.append(this_row) - - return output_rows, mapping_params['format'] - elif mapping_params['format'] == "json": - return result_markers, mapping_params['format'] - else: - return result_markers, None - - -def initialize_parameters(start_vars, dataset, this_trait): - mapping_params = {} - - mapping_params['format'] = "json" - if 'format' in start_vars: - mapping_params['format'] = start_vars['format'] - - mapping_params['limit_to'] = False - if 'limit_to' in start_vars: - if start_vars['limit_to'].isdigit(): - mapping_params['limit_to'] = int(start_vars['limit_to']) - - mapping_params['mapping_method'] = "gemma" - if 'method' in start_vars: - mapping_params['mapping_method'] = start_vars['method'] - - if mapping_params['mapping_method'] == "rqtl": - mapping_params['rqtl_method'] = "hk" - mapping_params['rqtl_model'] = "normal" - mapping_params['do_control'] = False - mapping_params['control_marker'] = "" - mapping_params['manhattan_plot'] = True - mapping_params['pair_scan'] = False - if 'rqtl_method' in start_vars: - mapping_params['rqtl_method'] = start_vars['rqtl_method'] - if 'rqtl_model' in start_vars: - mapping_params['rqtl_model'] = start_vars['rqtl_model'] - if 'control_marker' in start_vars: - mapping_params['control_marker'] = start_vars['control_marker'] - mapping_params['do_control'] = True - if 'pair_scan' in start_vars: - if start_vars['pair_scan'].lower() == "true": - mapping_params['pair_scan'] = True - - if 'interval_mapping' in start_vars: - if start_vars['interval_mapping'].lower() == "true": - mapping_params['manhattan_plot'] = False - elif 'manhattan_plot' in start_vars: - if start_vars['manhattan_plot'].lower() != "true": - mapping_params['manhattan_plot'] = False - - mapping_params['maf'] = 0.01 - if 'maf' in start_vars: - mapping_params['maf'] = start_vars['maf'] # Minor allele frequency - - mapping_params['use_loco'] = True - if 'use_loco' in start_vars: - if (start_vars['use_loco'].lower() == "false") or (start_vars['use_loco'].lower() == "no"): - mapping_params['use_loco'] = False - - mapping_params['num_perm'] = 0 - mapping_params['perm_check'] = False - if 'num_perm' in start_vars: - try: - mapping_params['num_perm'] = int(start_vars['num_perm']) - mapping_params['perm_check'] = "ON" - except: - mapping_params['perm_check'] = False - - mapping_params['transform'] = False - if 'transform' in start_vars: - mapping_params['transform'] = start_vars['transform'] - - mapping_params['genofile'] = False - if 'genofile' in start_vars: - mapping_params['genofile'] = start_vars['genofile'] - - return mapping_params - -def get_genofile_samplelist(dataset): - genofile_samplelist = [] - - genofile_json = dataset.group.get_genofiles() - for genofile in genofile_json: - if genofile['location'] == dataset.group.genofile and 'sample_list' in genofile: - genofile_samplelist = genofile['sample_list'] - - return genofile_samplelist |