padding = spacerLength
for s2, e2 in sv[record.CHROM].overlap((max(s1 - padding, 0), e1 + padding)):
for inv3to3 in svDups[(record.CHROM, s2, e2)] + [sv[record.CHROM][(s2, e2)]]:
if inv3to3['id'] == record.ID:
continue
spacer = min(abs(e1-s2), abs(e2-s1))
(recO, nestedO, recUnion, bpOffset, oLen) = overlapMetrics((s1, e1), (s2, e2))
cc = carrierConcordance(nonRefHap, inv3to3['nonRefHap'])
delLength = min(e1-s1, e2-s2)
if record.INFO['SVTYPE'] == "INV":
delLength = min(max(s1,s2)-min(s1,s2), max(e1,e2)-min(e1,e2))
if (spacer <= spacerLength) and (cc >= minCarrierConcordance) and (min(spacer, delLength) >= deletionLength) and (recO <= maxReciprocalOverlap):
svControlID1 = re.sub(r"^[A-Z0]*","", record.ID)
rdRatio1 = 1.0
if int(svControlID1) in control.keys():
rdRatio1 = altRefReadDepthRatio(rc, control[int(svControlID1)], hap)
svControlID2 = re.sub(r"^[A-Z0]*","", inv3to3['id'])
rdRatio2 = 1.0
if int(svControlID2) in control.keys():
rdRatio2 = altRefReadDepthRatio(inv3to3['rc'], control[int(svControlID2)], inv3to3['hap'])
print(record.CHROM, record.POS, record.INFO['END'], record.ID, record.CHROM, s2, e2, inv3to3['id'], spacer, delLength, cc, rdRatio1, rdRatio2)
if (not args.readDepth) or ((rdRatio1<0.8) and (rdRatio2<0.8)):
score = float(min(peCount, inv3to3['pe'])) * float(cc)
if score > invInfo['score']:
invInfo = {'id': inv3to3['id'], 'start': min(s1, s2), 'end': max(e1, e2), 'score': score}
if invInfo['score'] >= 0:
if not invRegion.has_key(record.CHROM):
invRegion[record.CHROM] = banyan.SortedDict(key_type=(int, int), alg=banyan.RED_BLACK_TREE, updator=banyan.OverlappingIntervalsUpdator)
G.add_node((record.ID, invInfo['id']))
G.node[(record.ID, invInfo['id'])]['Score'] = invInfo['score']
for invIStart, invIEnd in invRegion[record.CHROM].overlap((invInfo['start'], invInfo['end'])):
continue
if (not args.siteFilter) or (len(record.FILTER) == 0):
hap = dict()
rc = collections.defaultdict(int)
peCount = 0
for call in record.samples:
if call.called:
rc[call.sample] = call['RC']
hap[call.sample] = [int(gVal) for gVal in call['GT'].split('/')]
if (call.gt_type != 0) and (call['DV'] > 0):
peCount += call['DV']
if len(hap):
svStart = record.POS
svEnd = record.INFO['END']
svControlID = re.sub(r"^[A-Z0]*","", record.ID)
rdRatio = altRefReadDepthRatio(rc, sv[int(svControlID)], hap)
#print(record.CHROM, svStart, svEnd, record.ID, rdRatio, sep="\t")
if rdRatio is not None:
if ((record.INFO['SVTYPE'] == "DEL") and (rdRatio < 0.8)) or ((record.INFO['SVTYPE'] == "DUP") and (rdRatio >= 1.3) and (rdRatio <= 1.75)):
# Valid Call
if not cnvRegion.has_key(record.CHROM):
cnvRegion[record.CHROM] = banyan.SortedDict(key_type=(int, int), alg=banyan.RED_BLACK_TREE, updator=banyan.OverlappingIntervalsUpdator)
G.add_node(record.ID)
G.node[record.ID]['Score'] = peCount
for cnvIStart, cnvIEnd in cnvRegion[record.CHROM].overlap((svStart, svEnd)):
otherID = cnvRegion[record.CHROM][(cnvIStart, cnvIEnd)]
if overlapValid((svStart, svEnd), (cnvIStart, cnvIEnd), 0.1, 10000):
G.add_edge(record.ID, otherID)
cnvRegion[record.CHROM][(svStart, svEnd)] = record.ID
# Pick best deletion/duplication for all overlapping calls
padding = spacerLength
for s2, e2 in sv[record.CHROM].overlap((max(s1 - padding, 0), e1 + padding)):
for inv3to3 in svDups[(record.CHROM, s2, e2)] + [sv[record.CHROM][(s2, e2)]]:
if inv3to3['id'] == record.ID:
continue
spacer = min(abs(e1-s2), abs(e2-s1))
(recO, nestedO, recUnion, bpOffset, oLen) = overlapMetrics((s1, e1), (s2, e2))
cc = carrierConcordance(nonRefHap, inv3to3['nonRefHap'])
delLength = min(e1-s1, e2-s2)
if record.INFO['SVTYPE'] == "INV":
delLength = min(max(s1,s2)-min(s1,s2), max(e1,e2)-min(e1,e2))
if (spacer <= spacerLength) and (cc >= minCarrierConcordance) and (min(spacer, delLength) >= deletionLength) and (recO <= maxReciprocalOverlap):
svControlID1 = re.sub(r"^[A-Z0]*","", record.ID)
rdRatio1 = 1.0
if int(svControlID1) in control.keys():
rdRatio1 = altRefReadDepthRatio(rc, control[int(svControlID1)], hap)
svControlID2 = re.sub(r"^[A-Z0]*","", inv3to3['id'])
rdRatio2 = 1.0
if int(svControlID2) in control.keys():
rdRatio2 = altRefReadDepthRatio(inv3to3['rc'], control[int(svControlID2)], inv3to3['hap'])
print(record.CHROM, record.POS, record.INFO['END'], record.ID, record.CHROM, s2, e2, inv3to3['id'], spacer, delLength, cc, rdRatio1, rdRatio2)
if (not args.readDepth) or ((rdRatio1<0.8) and (rdRatio2<0.8)):
score = float(min(peCount, inv3to3['pe'])) * float(cc)
if score > invInfo['score']:
invInfo = {'id': inv3to3['id'], 'start': min(s1, s2), 'end': max(e1, e2), 'score': score}
if invInfo['score'] >= 0:
if not invRegion.has_key(record.CHROM):
invRegion[record.CHROM] = banyan.SortedDict(key_type=(int, int), alg=banyan.RED_BLACK_TREE, updator=banyan.OverlappingIntervalsUpdator)
G.add_node((record.ID, invInfo['id']))
G.node[(record.ID, invInfo['id'])]['Score'] = invInfo['score']
for invIStart, invIEnd in invRegion[record.CHROM].overlap((invInfo['start'], invInfo['end'])):
hap = dict()
rc = collections.defaultdict(int)
peCount = 0
for call in record.samples:
if call.called:
rc[call.sample] = call['RC']
hap[call.sample] = [
int(gVal) for gVal in call['GT'].split('/')
]
if (call.gt_type != 0) and (call['DV'] > 0):
peCount += call['DV']
if len(hap):
svStart = record.POS
svEnd = record.INFO['END']
svControlID = re.sub(r"^[A-Z0]*", "", record.ID)
rdRatio = altRefReadDepthRatio(rc, sv[int(svControlID)], hap)
#print(record.CHROM, svStart, svEnd, record.ID, rdRatio, sep="\t")
if rdRatio is not None:
if ((record.INFO['SVTYPE'] == "DEL") and
(rdRatio < 0.8)) or ((record.INFO['SVTYPE'] == "DUP")
and (rdRatio >= 1.3) and
(rdRatio <= 1.75)):
# Valid Call
if not cnvRegion.has_key(record.CHROM):
cnvRegion[record.CHROM] = banyan.SortedDict(
key_type=(int, int),
alg=banyan.RED_BLACK_TREE,
updator=banyan.OverlappingIntervalsUpdator)
G.add_node(record.ID)
G.node[record.ID]['Score'] = peCount
for cnvIStart, cnvIEnd in cnvRegion[
