def mutation_permuation_heat_wrapper((samples, genes, cnas, gene2length, bmr, gene2bmr,
gene2chromo, chromo2genes, cna_filter_threshold, min_freq)):
permuted_snvs = permute_snvs(samples, genes, gene2length, bmr, gene2bmr)
permuted_cnas = permute_cnas(cnas, gene2chromo, chromo2genes)
if cna_filter_threshold:
permuted_cnas = heat.filter_cnas(permuted_cnas, cna_filter_threshold)
return heat.mut_heat(len(samples), permuted_snvs, permuted_cnas, min_freq)
def load_mutation_heat(args):
samples = hnio.load_samples(args.sample_file) if args.sample_file else None
genes = hnio.load_genes(args.gene_file) if args.gene_file else None
snvs = hnio.load_snvs(args.snv_file, genes, samples)
cnas = hnio.load_cnas(args.cna_file, genes, samples)
if args.cna_filter_threshold:
cnas = hnheat.filter_cnas(cnas, args.cna_filter_threshold)
if not samples:
samples = set([mut.sample for mut in snvs + cnas])
heat = hnheat.mut_heat(len(samples), snvs, cnas, args.min_freq)
return heat, None
def load_mutation_heat(args):
samples = hnio.load_samples(args.sample_file) if args.sample_file else None
genes = hnio.load_genes(args.gene_file) if args.gene_file else None
snvs = hnio.load_snvs(args.snv_file, genes, samples)
cnas = hnio.load_cnas(args.cna_file, genes, samples)
if args.cna_filter_threshold:
cnas = hnheat.filter_cnas(cnas, args.cna_filter_threshold)
if not samples:
samples = set([mut.sample for mut in snvs + cnas])
heat = hnheat.mut_heat(len(samples), snvs, cnas, args.min_freq)
return heat, None
