diff options
| -rw-r--r-- | wqflask/wqflask/ctl/gn3_ctl_analysis.py | 79 |
1 files changed, 44 insertions, 35 deletions
diff --git a/wqflask/wqflask/ctl/gn3_ctl_analysis.py b/wqflask/wqflask/ctl/gn3_ctl_analysis.py index 113764a7..ba7d4971 100644 --- a/wqflask/wqflask/ctl/gn3_ctl_analysis.py +++ b/wqflask/wqflask/ctl/gn3_ctl_analysis.py @@ -1,4 +1,5 @@ import requests +import itertools from utility import genofile_parser from utility.tools import GN3_LOCAL_URL @@ -6,37 +7,53 @@ from utility.tools import locate from base.trait import create_trait from base.trait import retrieve_sample_data +from base import data_set -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(genofilelocation) - parser.process_csv() +def process_significance_data(significant_data): + """function to process significance the data for + datatables""" - # get marker and marker names + col_names = ["trait","marker","trait_2","LOD","dCor"] - return parser + data_set_rows = [[] for _ in range(len(significant_data["trait"]))] + + + + + return { + "col_names":[], + "" + } + +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"]) return { - "genotypes":list(itertools.chain(*markers)), - "markernames":markernames - "individuals":parser.individuals, + "genotypes": list(itertools.chain(*markers)), + "markernames": markernames, + "individuals": parser.individuals } -def parse_phenotype_data(trait_db_list): - """function to parse and generate phenodata""" +def parse_phenotype_data(trait_db_list, dataset, individuals): + """function to parse and generate phenodata""" traits = [] for trait in trait_db_list: @@ -50,16 +67,15 @@ def parse_phenotype_data(trait_db_list): else: traits.append("-999") - - # missing inviduals + # missing inviduals return { - "trait_db_list":trait_db_list, - "traits":traits + "trait_db_list": trait_db_list, + "traits": traits, + "individuals": individuals } - def parse_form_data(form_data: dict): """function to parse/validate form data input: dict containing required data @@ -68,11 +84,11 @@ def parse_form_data(form_data: dict): """ trait_db_list = [trait.strip() - for trait in requestform['trait_list'].split(',')] - form_data["trait_db_list"] = [x for x in trait_db_list if x] + for trait in form_data['trait_list'].split(',')] + 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(int(form_data["significance"])) + form_data["significance"] = float(form_data["significance"]) form_data["strategy"] = form_data["strategy"].capitalize() return form_data @@ -84,32 +100,25 @@ def run_ctl(requestform): ctl_api = f"{GN3_LOCAL_URL}/api/ctl/run_ctl" - form_data = parse_form_data(requestform) + 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]) - pheno_data = parse_geno_data(dataset.group.name) - - geno_data = parse_phenotype_data(trait_db_list) - - - pheno_data["individuals"] = geno_data["individuals"] + geno_data = parse_geno_data(dataset.group.name) + pheno_data = parse_phenotype_data( + trait_db_list, dataset, geno_data["individuals"]) response = requests.post(ctl_api, json={ - "genoData":geno_data, - "phenoData":pheno_data, + "genoData": geno_data, + "phenoData": pheno_data, - **form_data, + **form_data, }) # todo check for errors - response_data = response.json() - - print(">>>>>>>>>>>>>>>>>>>>>>",response_data) - - return "" + return response.json()
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