diff options
| -rw-r--r-- | wqflask/wqflask/ctl/gn3_ctl_analysis.py | 39 |
1 files changed, 24 insertions, 15 deletions
diff --git a/wqflask/wqflask/ctl/gn3_ctl_analysis.py b/wqflask/wqflask/ctl/gn3_ctl_analysis.py index 7af0013f..8f790597 100644 --- a/wqflask/wqflask/ctl/gn3_ctl_analysis.py +++ b/wqflask/wqflask/ctl/gn3_ctl_analysis.py @@ -10,11 +10,11 @@ from base.trait import retrieve_sample_data from base import data_set -def process_significance_data(significant_data): +def process_significance_data(dataset): col_names = ["trait", "marker", "trait_2", "LOD", "dcor"] - dataset_rows = [[] for _ in range(len(significant_data["trait"]))] + dataset_rows = [[] for _ in range(len(dataset["trait"]))] for col in col_names: - for (index, col_data) in enumerate(significant_data[col]): + for (index, col_data) in enumerate(dataset[col]): if col in ["dcor", "LOD"]: dataset_rows[index].append(round(float(col_data), 2)) else: @@ -27,6 +27,12 @@ def process_significance_data(significant_data): def parse_geno_data(dataset_group_name) -> dict: + """ + Args: + dataset_group_name: string name + + @returns : dict with keys genotypes,markernames & individuals + """ genofile_location = locate(dataset_group_name + ".geno", "genotype") parser = genofile_parser.ConvertGenoFile(genofile_location) parser.process_csv() @@ -46,9 +52,21 @@ def parse_geno_data(dataset_group_name) -> dict: } -def parse_phenotype_data(trait_db_list, dataset, individuals): +def parse_phenotype_data(trait_list, dataset, individuals): + """ + Args: + trait_list:list contains the traits + dataset: object + individuals:a list contains the individual vals + Returns: + traits_db_List:parsed list of traits + traits: list contains trait names + individuals + + """ + traits = [] - for trait in trait_db_list: + for trait in trait_list: if trait != "": ts = trait.split(':') gt = create_trait(name=ts[0], dataset_name=ts[1]) @@ -60,18 +78,13 @@ def parse_phenotype_data(trait_db_list, dataset, individuals): traits.append("-999") return { - "trait_db_list": trait_db_list, + "trait_db_list": trait_list, "traits": traits, "individuals": individuals } def parse_form_data(form_data: dict): - """function to parse/validate form data - input: dict containing required data - output: dict with parsed data - - """ trait_db_list = [trait.strip() for trait in form_data['trait_list'].split(',')] @@ -96,8 +109,6 @@ def run_ctl(requestform): pheno_data = parse_phenotype_data( trait_db_list, dataset, geno_data["individuals"]) - # todo refactor this chunk;;similar to wgcna check - try: response = requests.post(ctl_api, json={ @@ -119,5 +130,3 @@ def run_ctl(requestform): return { "error": "A connection error to perform computation occurred" } - - |