diff options
| -rw-r--r-- | wqflask/wqflask/api/mapping.py | 62 |
1 files changed, 48 insertions, 14 deletions
diff --git a/wqflask/wqflask/api/mapping.py b/wqflask/wqflask/api/mapping.py index d1cc368e..5ffcbd55 100644 --- a/wqflask/wqflask/api/mapping.py +++ b/wqflask/wqflask/api/mapping.py @@ -23,26 +23,46 @@ def do_mapping_for_api(start_vars): samples = [] vals = [] - for sample in dataset.group.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") - mapping_params = initialize_parameters(start_vars, dataset, this_trait) - # ZS: It seems to take an empty string as default. This should probably be changed. + genofile_samplelist = [] + if mapping_params['genofile']: + dataset.group.genofile = mapping_params['genofile'] + genofile_samplelist = get_genofile_samplelist(dataset) + + logger.debug("SAMPLES:", genofile_samplelist) + + if (len(genofile_samplelist) > 0): + for sample in genofile_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: + for sample in dataset.group.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") + + # 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"] - # ZS: gemma_mapping returns both results and the filename for LOCO, so need to only grab the former for api + # 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] @@ -138,4 +158,18 @@ def initialize_parameters(start_vars, dataset, this_trait): except: mapping_params['perm_check'] = False + 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 |