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)
