Miscan API

MiScan utils

utils.exists_or_mkdir(path[, verbose]) Check a folder by given name, if not exist, create the folder and return False, if directory exists, return True.
utils.file_exists(filepath) Check whether a file exists by given file path.
utils.get_data() get dependency data config

MiScan model

model.build_model

MiScan Core

core.vcf_to_sparse(outDir, inFeaID, …) convert the vcf to a feature matrix, matrix.mtx :param outDir: output directory :param inFeaID: 13885fea_exon_cut_100bp_2sample.txt in dependency_data :param inFeaBed: tcga_13885fea_exon_cut_100bp.bed in dependency_data :param inVcf: the input vcf file path :param featureID: featureID.bed in dependency_data :return:
core.prediction(outDir, model_weight) predict single sample breast cancer risk
core.generate_report(inDir, outDir, y_pred_pat) generate report for single sample, including Cancer Risk Prediction | Top Gene Mutation Sites
core.miscan_main(outDir, inVcf[, model_weight]) website sanctuary analysis core callable func :param model_weight: path of model weights :param outDir: temp, final result dir :param inVcf:input vcf full absolute path :return:no return