def get_haplotype_copy_numbers_from_spanning_reads(self, spanning_reads):
if len(spanning_reads) < 1:
logging.info('There is no spanning read')
return None
max_length = 0
for read in spanning_reads:
if len(read) - 100 > max_length:
max_length = len(read) - 100
max_copies = int(
round(max_length / float(len(self.reference_vntr.pattern))))
max_copies = min(max_copies,
2 * len(self.reference_vntr.get_repeat_segments()))
vntr_matcher = self.build_vntr_matcher_hmm(max_copies)
haplotyper = PacBioHaplotyper(spanning_reads)
haplotypes = haplotyper.get_error_corrected_haplotypes()
copy_numbers = []
for haplotype in haplotypes:
# print('haplotype: %s' % haplotype)
logp, vpath = vntr_matcher.viterbi(haplotype)
rev_logp, rev_vpath = vntr_matcher.viterbi(
str(Seq(haplotype).reverse_complement()))
if logp < rev_logp:
vpath = rev_vpath
copy_numbers.append(get_number_of_repeats_in_vpath(vpath))
return copy_numbers
def find_ru_counts_with_naive_approach(self, length_dist, spanning_reads):
haplotyper = PacBioHaplotyper(spanning_reads)
haplotypes = haplotyper.get_error_corrected_haplotypes(1)
flanking_region_lengths = []
new_spanning_reads = []
if len(haplotypes) == 0:
return None
self.check_if_flanking_regions_align_to_str(haplotypes[0].upper(),
flanking_region_lengths,
new_spanning_reads)
reverse_complement_str = str(Seq(haplotypes[0]).reverse_complement())
self.check_if_flanking_regions_align_to_str(
reverse_complement_str.upper(), flanking_region_lengths,
new_spanning_reads)
if len(flanking_region_lengths) > 0:
return [
round(flanking_region_lengths[0] /
len(self.reference_vntr.pattern))
] * 2
else:
return None