def get_filtered_phased_het_trio_variants(trio_vcf, trio_filtered_het_phased_vcf, sample_name):
vcf_in = VariantFile(trio_vcf)
vcf_in.subset_samples([sample_name])
vcf_out = VariantFile(trio_filtered_het_phased_vcf, 'w', header=vcf_in.header)
for rec in vcf_in.fetch():
if rec.filter.keys()[0] == 'PASS':
rec_sample = rec.samples[0]
if rec_sample.phased and rec_sample['GT'][0] != rec_sample['GT'][1]:
rec.samples[0].update({'PS':1})
vcf_out.write(rec)
return 0
def read_vcf(vcf, sample) :
"""Reads a VCF and fetches relevant information to a Pandas DataFrame"""
vcf_in = VariantFile(vcf) # auto-detect input format
vcf_in.subset_samples([sample])
# Variant sites for probability computation (and later modelisation)
VariantSites = {"CHROM":[], "POS":[], "TYPE":[], "DP":[], "MAF":[], "GT":[], "QUAL":[], "ALS":[]}
for i, rec in enumerate(vcf_in) : # For each record in vcf
if i % 200000 == 0 :
print("Elapsed records: {}".format(i))
gt = rec.samples[sample]["GT"] # Get sample GT
if len(set(gt)) == 1 :
continue # SKIP IF HOMOZYGOUS
VariantSites["CHROM"].append(rec.chrom) # Add record CHROM
VariantSites["POS"].append(rec.pos) # Add record POS
als = [x for n, x in enumerate(rec.alleles) if n in gt] # Get record position
VariantSites["ALS"].append(als) # Add record alleles
VariantSites["GT"].append(gt) # Add sample GT
if "<NON_REF>" in als : # In case undefined allele
vtype = "U"
elif any(len(x) > 1 for x in als) or "*" in als : # In case any is a deletion or is an insertion
vtype = "I"
else : # In case not non-ref and not an INDEL
vtype = "S"
VariantSites["TYPE"].append(vtype) # Add sample type
try : # Add sample DP and compute Min AF based on allele reads frequencies. If AD or DP is unavailable fills with None
dp = rec.samples[sample]["DP"]
VariantSites["DP"].append(dp)
try :
min_ad = min(rec.samples[sample]["AD"])
min_af = float(min_ad/dp)
VariantSites["MAF"].append(min_af)
except :
VariantSites["MAF"].append(None)
except :
VariantSites["DP"].append(None)
try : # Add record QUAL at this position
VariantSites["QUAL"].append(rec.qual)
except :
VariantSites["QUAL"].append(None)
return pd.DataFrame.from_dict(VariantSites)
def get_hets(vcf, sample):
"""extract heterozygous STRs and SNPs from the vcf"""
vcf = VariantFile(vcf)
vcf.subset_samples([sample])
# iterate through each variant record in the VCF
# TODO: make sure you're considering cases where the POS is duplicated
for rec in vcf.fetch():
variant = rec.samples[sample]
is_het = variant['GT'][0] != variant['GT'][1]
is_snp = not ((len(variant.alleles[0]) - len(variant.alleles[1])))
# limit our analysis to only variants that are heterozygous
# and they must be either STRs or SNPs
if (is_het and (is_snp or rec.id.startswith("STR_"))):
yield rec
def main(varfile, keep, outprefix):
"""
输出sweepfinder2的allele frequency file文件
要求输入的vcf文件没有缺失
输出文件中会把alt allele count为0的过滤掉
"""
varin = VariantFile(varfile)
samples = [x.strip() for x in open(keep).readlines()]
varin.subset_samples(samples)
print(f'keep samples:\n{samples}')
ss = len(samples) * 2 # sample size
with open(f'{outprefix}.SF', 'w') as f:
f.write('position\tx\tn\tfolded\n')
for rec in varin.fetch():
gts = [s['GT'] for s in rec.samples.values()]
gts = np.array(gts, dtype='int8').flatten()
ac = np.sum(gts) # alt allele count
if ac > 0:
f.write(f'{rec.pos}\t{ac}\t{ss}\t1\n')