def check_concordancies(self, data_list, assays, chipval):
hwe_values = [0.0] * len(data_list)
maf_values = [0.0] * len(data_list)
obs = [0.0] * 3
exp = [0.0] * 3
allele_ref_1 = ""
allele_alt_1 = ""
allele_ref_2 = ""
allele_alt_2 = ""
#print "CHECK_CONC:", len(data_list)
for i, vcf_record in enumerate(data_list):
if len(vcf_record) > 0:
vcfr = VCFrecord(vcf_record)
probidx = vcfr.get_probidx()
homref_count, het_count, homalt_count, nc_count, miss_count = self.vcfr.get_allele_counts_from_array(
data)
allele_a, allele_b = vcfr.get_alleles()
if allele_ref_1 == "":
allele_ref_1 = allele_a
allele_alt_1 = allele_b
# Add 1 to prevent 0-divide
obs[0] = homref_count + 1
obs[1] = het_count + 1
obs[2] = homalt_count + 1
else:
allele_ref_2 = allele_a
allele_alt_2 = allele_b
exp[0] = homref_count + 1
exp[1] = het_count + 1
exp[2] = homalt_count + 1
if (allele_ref_1 != allele_ref_2) or (allele_alt_1 !=
allele_alt_2):
varid = vcfr.get_varid(data)
posn = vcfr.get_posn(data)
self.allele_discord_count += 1
logging.info(
"Allele discordancy: assay1=%s, assay2=%s, varid=%s, posn=%d, ref1=%s, alt1=%s, ref2=%s, alt2=%s",
assays[0], assays[i], varid, int(posn),
allele_ref_1, allele_alt_1, allele_ref_2,
allele_alt_2)
#print "Allele discord"
return False
chi_stat, chi_p_value = chisquare(obs, f_exp=exp)
varid = vcfr.get_varid(data)
posn = vcfr.get_posn(data)
if chi_p_value < chipval:
self.chisq_count += 1
logging.info(
"CHI SQ test REJECT: assay1=%s, assay2=%s, varid=%s, posn=%d, chistat=%f, p_val=%e, chipval=%e, obs=%s, exp=%s, at %d",
assays[0], assays[i], varid, int(posn), chi_stat,
chi_p_value, chipval, str(obs), str(exp), i)
#print "CHISQ discord"
return False
logging.info(
"CHI SQ test OK: assay1=%s, assay2=%s, varid=%s, posn=%d, chistat=%f, p_val=%e, obs=%s, exp=%s, at %d",
assays[0], assays[i], varid, int(posn), chi_stat,
chi_p_value, str(obs), str(exp), i)
return True
def process_variant_detail_vcf(self, record, assaytype):
"""Process info file variant detail records
Set up a json-stype document and add it to the
variant buffer
"""
doc = {}
doc["assaytype"] = assaytype
vcfr = VCFrecord(record)
prfx, sfx = vcfr.get_prfx_sfx()
doc["rsid"] = vcfr.get_varid()
# always store chromosome as a 2-digit string
doc["chromosome"] = "%.2d" % (int(vcfr.get_chr()))
alleleA, alleleB = vcfr.get_alleles()
doc["alleleA"] = alleleA
doc["alleleB"] = alleleB
doc["position"] = vcfr.get_posn_as_int()
try:
doc["ref_maf"] = float(vcfr.get_info_value("RefPanelAF"))
except:
pass
try:
doc["info"] = float(vcfr.get_info_value("INFO"))
except:
doc["info"] = 1.0
self.variantbuff.append(doc)
def get_dbsnp_rsid(dbsnpfile, chrom, posn):
dbsnprec = dbsnpfile.get_dbsnp_file_record(options.dbsnpfile, chrom, int(posn))
rsid = ""
refallele = ""
if dbsnprec != None:
dbvcf = VCFrecord(dbsnprec)
rsid = dbvcf.get_varid()
refallele, altallele = dbvcf.get_alleles()
return rsid, refallele
def main():
mafh = Mafhelper()
hweh = Hwehelper()
in_count = 0
hdr_count = 0
homr_total = 0
het_total = 0
homa_total = 0
virt_nc_total = 0
miss_total = 0
print "SNPId,AssayType,chr,pos,REF,ALT,Minor,MAF,CallRate,HWE_pval"
for line in sys.stdin:
line = line.strip()
in_count += 1
if line.startswith("#"):
hdr_count += 1
continue
vcfr = VCFrecord(line)
varid = vcfr.get_varid_ukb()
chromosome = vcfr.get_chr()
posn = vcfr.get_posn_as_int()
ref, alt = vcfr.get_alleles()
homref_count, het_count, homalt_count, virt_nc_count, miss_count = vcfr.get_allele_counts()
call_count = homref_count + het_count + homalt_count
#nocall_count = virt_nc_count + miss_count
nocall_count = virt_nc_count
call_rate = float(call_count) / float(call_count + nocall_count)
homr_total += homref_count
het_total += het_count
homa_total += homalt_count
virt_nc_total += virt_nc_count
miss_total += miss_count
try:
hwe = hweh.HWE_exact(het_count, homref_count, homalt_count, call_count)
maf, ma = mafh.maf(het_count, homref_count, ref, homalt_count, alt, virt_nc_count)
except ZeroDivisionError:
logging.info("DIV 0 error at %d (%d), where hom_r=%d, het=%d, home_a=%d, cc=%d", in_count, posn, homref_count, het_count, homalt_count, call_count)
print "%s,combo,%s,%d,%s,%s,%s,%s,%.3f,%s" % (varid, chromosome, posn, ref, alt, ma, maf, call_rate, hwe)
return in_count, hdr_count, homr_total, het_total, homa_total, virt_nc_total, miss_total
def main(options):
hdrData = ["id"]
sampleDict = {}
colPosns = {}
RefAlleleDict = {}
AltAlleleDict = {}
count = 0
mafh = Mafhelper()
for line in sys.stdin:
line = line.strip()
if (line.startswith('##')):
pass
else:
vcfr = VCFrecord(line)
prfx, sfx = vcfr.get_prfx_sfx()
#print prfx
if (line.startswith('#')):
# Parse out the header record.
for i, col_hdr in enumerate(sfx):
colPosns[i] = col_hdr
sampleDict[col_hdr] = []
else:
flip = False
varid = vcfr.get_varid_ukb()
#logging.info("varid=%s", varid)
ref, alt = vcfr.get_alleles()
probidx = vcfr.get_probidx()
hdr_allele = alt
homref_count, het_count, homalt_count, nc_count, miss_count = vcfr.get_allele_counts(
)
call_count = homref_count + het_count + homalt_count
maf, ma = mafh.maf(het_count, homref_count, ref, homalt_count,
alt, nc_count)
RefAlleleDict[varid] = ref
AltAlleleDict[varid] = alt
#if ma == ref:
# flip = True
# hdr_allele = ref
# logging.info("FLIP for %s, %s, %s", varid, ref, alt)
hdrData.append(varid)
for i, str_geno in enumerate(sfx):
if str_geno != ".":
geno = str_geno.split(":")
max_prob, max_idx = get_max_prob(geno, probidx)
i_call = icalls[geno[0]]
if flip == True:
if i_call == "0":
i_call == "2"
elif i_call == "2":
i_call = "0"
sampleDict[colPosns[i]].append(str(i_call))
else:
sampleDict[colPosns[i]].append("")
print ",".join(hdrData)
for samp in sampleDict:
count += 1
print ",".join([samp] + sampleDict[samp])
return count
