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_file else []
if args.cna_filter_threshold:
cnas = hnheat.filter_cnas(cnas, args.cna_filter_threshold)
if not samples:
samples = set([snv.sample for snv in snvs] + [cna.sample for cna in cnas])
return hnheat.mut_heat(len(samples), snvs, cnas, args.min_freq), None
def load_mutation_heat(args):
genes = hnio.load_genes(args.gene_file) if args.gene_file else None
samples = hnio.load_samples(args.sample_file) if args.sample_file else None
snvs = hnio.load_snvs(args.snv_file, genes, samples)
cnas = hnio.load_cnas(args.cna_file, genes,
samples) if args.cna_file else []
if args.cna_filter_threshold:
cnas = hnheat.filter_cnas(cnas, args.cna_filter_threshold)
if not samples:
samples = set([snv.sample
for snv in snvs] + [cna.sample for cna in cnas])
if not genes:
genes = set([snv.gene for snv in snvs] + [cna.gene for cna in cnas])
return hnheat.mut_heat(genes, len(samples), snvs, cnas, args.min_freq)