diff options
| -rw-r--r-- | wqflask/wqflask/correlation/show_corr_results.py | 46 |
1 files changed, 40 insertions, 6 deletions
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 7623e18e..dfa48800 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -31,6 +31,7 @@ from wqflask.correlation.pre_computes import cache_new_traits_metadata from utility.authentication_tools import check_resource_availability from utility import hmac +from utility.type_checking import get_float, get_int, get_string def set_template_vars(start_vars, correlation_data): @@ -51,6 +52,7 @@ def set_template_vars(start_vars, correlation_data): target_dataset_ob = create_dataset(correlation_data['target_dataset']) correlation_data['target_dataset'] = target_dataset_ob.as_dict() correlation_data['table_json'] = correlation_json_for_table( + start_vars, correlation_data, correlation_data['this_trait'], correlation_data['this_dataset'], @@ -73,7 +75,7 @@ def set_template_vars(start_vars, correlation_data): return correlation_data -def correlation_json_for_table(correlation_data, this_trait, this_dataset, target_dataset_ob): +def correlation_json_for_table(start_vars, correlation_data, this_trait, this_dataset, target_dataset_ob): """Return JSON data for use with the DataTable in the correlation result page Keyword arguments: @@ -93,6 +95,20 @@ def correlation_json_for_table(correlation_data, this_trait, this_dataset, targe dataset_metadata = correlation_data["traits_metadata"] + min_expr = get_float(start_vars, 'min_expr') + p_range_lower = get_float(start_vars, 'p_range_lower', -1.0) + p_range_upper = get_float(start_vars, 'p_range_upper', 1.0) + + if ('loc_chr' in start_vars and + 'min_loc_mb' in start_vars and + 'max_loc_mb' in start_vars): + + location_chr = get_string(start_vars, 'loc_chr') + min_location_mb = get_int(start_vars, 'min_loc_mb') + max_location_mb = get_int(start_vars, 'max_loc_mb') + else: + location_chr = min_location_mb = max_location_mb = None + for i, trait_dict in enumerate(corr_results): trait_name = list(trait_dict.keys())[0] trait = trait_dict[trait_name] @@ -104,14 +120,32 @@ def correlation_json_for_table(correlation_data, this_trait, this_dataset, targe get_qtl_info=True) target_trait = jsonable(target_trait_ob, target_dataset_ob) new_traits_metadata[trait_name] = target_trait - else: - if target_dataset['type'] == "Publish": - permissions = check_resource_availability(target_dataset_ob, trait_name) - if permissions['metadata'] == "no-access": + + if (float(trait.get('corr_coefficient',0.0)) >= p_range_lower and + float(trait.get('corr_coefficient',0.0)) <= p_range_upper): + + if (target_dataset['type'] == "ProbeSet" or target_dataset['type'] == "Publish") and bool(target_trait['mean']): + if (min_expr != None) and (float(target_trait['mean']) < min_expr): continue - if target_trait['view'] == False: + if target_dataset['type'] == "ProbeSet" or target_dataset['type'] == "Geno": + if start_vars['location_type'] == "gene": + if location_chr != None and (target_trait['chr'] != location_chr): + continue + if (min_location_mb != None) and (float(target_trait['mb']) < float(min_location_mb)): + continue + if (max_location_mb != None) and (float(target_trait['mb']) > float(max_location_mb)): + continue + else: + if location_chr != None and (target_trait['lrs_chr'] != location_chr): + continue + if (min_location_mb != None) and (float(target_trait['lrs_mb']) < float(min_location_mb)): + continue + if (max_location_mb != None) and (float(target_trait['lrs_mb']) > float(max_location_mb)): + continue + else: continue + results_dict = {} results_dict['index'] = i + 1 results_dict['trait_id'] = target_trait['name'] |