def writeVariants(self, variants):
for var in variants:
pos = var.refStart
ref = ""
alt = ""
labels = (1, 2)
# insertion or deletion
if var.refSeq == "" or var.readSeq1 == "" or \
(var.isHeterozygous and var.readSeq2 == ""):
# we're anchored on the previous base so no 0- to 1-indexing
# correction required
ref = var.refPrev + var.refSeq
if var.isHeterozygous:
alt = ",".join(var.readPrev + seq for seq in (var.readSeq1, var.readSeq2))
else:
alt = var.readPrev + var.readSeq1
# substitution
else:
# due to 1-indexing, pos needs to be incremented
pos += 1
ref = var.refSeq
if var.isHeterozygous:
alt = ",".join(seq for seq in (var.readSeq1, var.readSeq2))
if var.refSeq == var.readSeq1:
# first variant is same as wildtype
alt = var.readSeq2
labels = (2,)
elif var.refSeq == var.readSeq2:
# second variant is same as wildtype
alt = var.readSeq1
labels = (1,)
else:
# both variants differ from wildtype
alt = ",".join(seq for seq in (var.readSeq1, var.readSeq2))
else:
alt = var.readSeq1
freq = vcfVariantFrequency(var=var, labels=labels)
info = "DP={0}".format(var.coverage)
if freq:
info = info + ";" + freq
# failed filters
failedFilters = []
if var.confidence < self._minConfidence:
failedFilters.append(self._minConfidenceFilterID)
if var.coverage < self._minCoverage:
failedFilters.append(self._minCoverageFilterID)
filterText = ";".join(failedFilters) if failedFilters else "PASS"
print("{chrom}\t{pos}\t{id}\t{ref}\t{alt}\t{qual}\t{filter}\t{info}".format(
chrom=reference.idToFullName(var.refId),
pos=pos,
id=".",
ref=ref,
alt=alt,
qual=var.confidence,
filter=filterText,
info=info), file=self._vcfFile)
def writeVariants(self, variants):
for var in variants:
pos = var.refStart
ref = ""
alt = ""
labels = (1, 2)
# insertion or deletion
if var.refSeq == "" or var.readSeq1 == "" or \
(var.isHeterozygous and var.readSeq2 == ""):
# we're anchored on the previous base so no 0- to 1-indexing
# correction required
ref = var.refPrev + var.refSeq
if var.isHeterozygous:
alt = ",".join(var.readPrev + seq
for seq in (var.readSeq1, var.readSeq2))
else:
alt = var.readPrev + var.readSeq1
# substitution
else:
# due to 1-indexing, pos needs to be incremented
pos += 1
ref = var.refSeq
if var.isHeterozygous:
alt = ",".join(seq for seq in (var.readSeq1, var.readSeq2))
if var.refSeq == var.readSeq1:
# first variant is same as wildtype
alt = var.readSeq2
labels = (2, )
elif var.refSeq == var.readSeq2:
# second variant is same as wildtype
alt = var.readSeq1
labels = (1, )
else:
# both variants differ from wildtype
alt = ",".join(seq
for seq in (var.readSeq1, var.readSeq2))
else:
alt = var.readSeq1
freq = vcfVariantFrequency(var=var, labels=labels)
info = "DP={0}".format(var.coverage)
if freq:
info = info + ";" + freq
print(
"{chrom}\t{pos}\t{id}\t{ref}\t{alt}\t{qual}\t{filter}\t{info}".
format(chrom=reference.idToFullName(var.refId),
pos=pos,
id=".",
ref=ref,
alt=alt,
qual=var.confidence,
filter="PASS",
info=info),
file=self._vcfFile)
def toGffRecord(var):
varType = var.variantType
gffType = varType.lower()
gffStart = (var.refStart + 1) if (var.refSeq != "") else var.refStart
gffEnd = var.refEnd if (var.refSeq != "") else var.refStart
gffFreq = gffVariantFrequency(var)
record = Gff3Record(reference.idToFullName(var.refId), gffStart, gffEnd, gffType)
record.reference = var.refSeq or "."
record.variantSeq = gffVariantSeq(var)
if gffFreq:
record.frequency = gffFreq
record.coverage = var.coverage
record.confidence = var.confidence
if var.annotations:
for (k, v) in var.annotations:
record.put(k, v)
return record