def get_tract_snps(vcf, chrom, start, end):
''' (str, str, int, int) -> int
helper function that returns # of variants in given window
'''
v = VCF(vcf)
region = '{chrom}:{start}-{end}'.format(chrom=chrom, start=start, end=end)
snp_count = len([record for record in v.__call__(region)])
return snp_count
def count_window(vcf, chrom, start, end):
''' (str, str, int, int) -> int
helper function for get_density that counts SNPs
in a given window
'''
v = VCF(vcf)
region = '{chrom}:{start}-{end}'.format(chrom=chrom, start=start, end=end)
snp_count = len([record for record in v.__call__(region)])
return snp_count
def count_window_snps(vcf, start, read_length, insert_size, chrom):
''' (str, int, int, int, str) -> int, int
helper function for parse_windows below
counts SNPs in both left and right read given start point + read_length + ins size
'''
window_left = (start, start + read_length)
right_start = window_left[1] + insert_size
window_right = (right_start, right_start + read_length)
left_count, right_count = 0, 0
vcfin = VCF(vcf)
range_str = '{0}:{1}-{2}'
for record in vcfin.__call__(range_str.format(chrom, *window_left)):
left_count += 1
for record in vcfin.__call__(range_str.format(chrom, *window_right)):
right_count += 1
return left_count, right_count
def vcf_to_fasta_markers(args):
if args.samples:
samples = open(args.samples).read().strip().split("\n")
elif args.nsamples:
samples = get_samples_from_bcf(args.vcf)[:args.nsamples]
else:
samples = get_samples_from_bcf(args.vcf)
if args.fasta == "-":
fasta_in = sys.stdin
else:
fasta_in = open(args.fasta)
pos = 0
if args.save_fasta:
fasta_out = open(args.out + ".from_vcf.fa", "w")
marker_out = open(args.out + ".markers", "wb")
# First, feed the reference sequence to the thing:
for name, seq, qual in readfq(fasta_in):
pos += len(seq)
to_write = ">{}\n{}\n".format(name, seq)
if args.save_fasta:
fasta_out.write(to_write)
yield to_write.encode()
fasta_in.seek(0)
# Then feed in each haplotype
for sample in samples:
for i in range(2): # process two haplotypes
for name, seq, qual in readfq(fasta_in):
prec_end = 0
prec_start = 0
to_write = ">{}.{}.{}\n".format(sample, i + 1, name)
if args.save_fasta:
fasta_out.write(to_write)
yield to_write.encode()
bcf = VCF(args.vcf)
bcf.set_samples([sample])
# recs = bcf.__call__(contig)
recs = bcf.__call__(name)
for rec in recs:
gts = rec.genotypes[0]
if (len(gts) != 3):
die("error: number of genotypes for {} at marker {} is not 2!"
.format(sample, rec.ID))
if gts[i]:
if rec.start in range(prec_start, prec_end):
sys.stderr.write(
"warning: skipping {} at {}:{} because it overlaps a previous marker\n"
.format(rec.ID, rec.CHROM, rec.start))
continue
pos += rec.start - prec_end # ffwd current position
if len(rec.REF) >= len(
rec.ALT[gts[i] - 1]): # del and snp
write_marker(marker_out, pos, rec.start, gts[i],
args.bytes, args.endian)
pos += 1
elif len(rec.REF) < len(rec.ALT[gts[i] - 1]):
# insertion
ins_size = len(rec.ALT[gts[i] - 1]) - len(
rec.REF) + 1
for j in range(ins_size):
write_marker(marker_out, pos, rec.start,
gts[i], args.bytes, args.endian)
pos += 1
# to_write = str(seq[prec_end:rec.start]) + str(rec.ALT[gts[i]-1])
to_write = seq[prec_end:rec.start] + rec.ALT[gts[i] -
1]
if args.save_fasta:
fasta_out.write(to_write)
yield to_write.encode()
prec_start = rec.start
# prec_end skips over to position just after record
prec_end = rec.start + len(rec.REF)
bcf.close()
pos += len(seq) - prec_end
to_write = seq[prec_end:] + "\n"
if args.save_fasta:
fasta_out.write(to_write)
yield to_write.encode()
fasta_in.seek(0)
if args.save_fasta:
fasta_out.close()
marker_out.close()
fasta_in.close()
