diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/ctl/gn3_ctl_analysis.py | 22 |
1 files changed, 2 insertions, 20 deletions
diff --git a/wqflask/wqflask/ctl/gn3_ctl_analysis.py b/wqflask/wqflask/ctl/gn3_ctl_analysis.py index 4afae119..67f76a30 100644 --- a/wqflask/wqflask/ctl/gn3_ctl_analysis.py +++ b/wqflask/wqflask/ctl/gn3_ctl_analysis.py @@ -11,21 +11,13 @@ from base import data_set def process_significance_data(significant_data): - """function to process significance the data for - datatables""" - col_names = ["trait", "marker", "trait_2", "LOD", "dcor"] - dataset_rows = [[] for _ in range(len(significant_data["trait"]))] - for col in col_names: for (index, col_data) in enumerate(significant_data[col]): - if col in ["dcor", "LOD"]: - dataset_rows[index].append(round(float(col_data), 2)) else: - dataset_rows[index].append(col_data) return { @@ -35,16 +27,11 @@ def process_significance_data(significant_data): def parse_geno_data(dataset_group_name) -> dict: - """function to parse geno file data""" genofile_location = locate(dataset_group_name + ".geno", "genotype") parser = genofile_parser.ConvertGenoFile(genofile_location) - parser.process_csv() - markers = [] - markernames = [] - for marker in parser.markers: markernames.append(marker["name"]) markers.append(marker["genotypes"]) @@ -60,8 +47,6 @@ def parse_geno_data(dataset_group_name) -> dict: def parse_phenotype_data(trait_db_list, dataset, individuals): - """function to parse and generate phenodata""" - traits = [] for trait in trait_db_list: if trait != "": @@ -90,27 +75,24 @@ def parse_form_data(form_data: dict): trait_db_list = [trait.strip() for trait in form_data['trait_list'].split(',')] - form_data["trait_db_list"] = [x for x in trait_db_list if x] + form_data["trait_db_list"] = [x for x in trait_db_list if x] form_data["nperm"] = int(form_data["nperm"]) form_data["significance"] = float(form_data["significance"]) form_data["strategy"] = form_data["strategy"].capitalize() + return form_data def run_ctl(requestform): """function to make an api call to gn3 and run ctl""" - ctl_api = f"{GN3_LOCAL_URL}/api/ctl/run_ctl" form_data = parse_form_data(requestform.to_dict()) - trait_db_list = form_data["trait_db_list"] dataset = data_set.create_dataset(trait_db_list[0].split(":")[1]) - geno_data = parse_geno_data(dataset.group.name) - pheno_data = parse_phenotype_data( trait_db_list, dataset, geno_data["individuals"]) |