def get_vcf_chromosome_map(datasets, chromosome):
all_vcfs = list(set(loc for d in datasets for loc in d['vcfLocations']['SS']))
vcf_chromosome_map = {}
for vcf in all_vcfs:
vcf_chromosomes = get_vcf_chromosomes(vcf)
vcf_chromosome_map[vcf] = get_matching_chromosome(vcf_chromosomes,
chromosome)
return vcf_chromosome_map
def get_translated_regions(location):
vcf_chromosomes = get_vcf_chromosomes(location)
vcf_regions = []
for target_chromosome, region_list in regions.items():
chromosome = get_matching_chromosome(vcf_chromosomes, target_chromosome)
if not chromosome:
continue
vcf_regions += ['{}:{}'.format(chromosome, region)
for region in region_list]
return vcf_regions
def get_translated_regions(location):
vcf_chromosomes = get_vcf_chromosomes(location)
regions = []
for target_chromosome in CHROMOSOMES:
chromosome = get_matching_chromosome(vcf_chromosomes, target_chromosome)
if not chromosome:
continue
start = 0
length, _ = vcf_chromosomes[chromosome]
length_mbp = length / 1000000
while start < length_mbp:
mbp_left = (length_mbp - start)
region_size = min(MAX_SLICE_SIZE_MBP, mbp_left)
if int(region_size) == region_size:
region_size = int(region_size)
regions.append(('{}:{}'.format(chromosome, start),
region_size))
start += region_size
return regions