def save_chromosome_metadata(self): """ create and save a list of VCF Filenames for each contig """ df = self.create_chromosome_metadata() hvb.try_make_dirs(self.out_dir) fname = os.path.join(self.out_dir, "chromosome_metadata_m{}.tsv".format(self.genotype_method)) df.to_csv(fname, sep="\t")
def save_individual_metadata(self): """ saves the metadata matrix to the folder <data_dir>/metadata/method_{}/ this metadata matrix should be produced once and used for all analyses """ hvb.try_make_dirs(self.out_dir) out_fname = os.path.join(self.out_dir, "individual_metadata_m{}.tsv".format(self.genotype_method)) metadata = self.create_individual_metadata_df() metadata.to_csv(out_fname, sep="\t")
def save_genotype_data(self,chromosome,qualityfilter=0,minDepth=0): meta_fname=os.path.join(self.meta_dir,"snp_metadata_m{}_{}.tsv".format(self.genotype_method,chromosome)) hvb.try_make_dirs(os.path.dirname(meta_fname)) geno_fname=os.path.join(self.data_dir,"hs_data/genotype_method_{}/".format(self.genotype_method),\ "genotype_mat_ancestral_m{}_{}.tsv".format(self.genotype_method,chromosome)) hvb.try_make_dirs(os.path.dirname(geno_fname)) dd=self.extract_genotype_data(chromosome,qualityfilter=qualityfilter,minDepth=minDepth) genotype_df=self.create_genotype_df(dd) metadata_df=self.add_ancestral_to_metadata(chromosome,self.create_genotype_metadata(dd)) genotype_df=self.polarise_ancestral_genotype(genotype_df,metadata_df) metadata_df.to_csv(meta_fname,sep='\t') hvb.save_genotype(genotype_df,geno_fname)