def __init__(self, region, alignDistance, fasta):
breakpoints = [
Locus(region.chr(), region.start(), region.start(), "+"),
Locus(region.chr(), region.end(), region.end(), "+")
]
super(Inversion, self).__init__(breakpoints, alignDistance, fasta)
self.region = region
def getReads(variant,
bam,
minmapq,
pair_minmapq,
searchDistance,
single_ended=False,
include_supplementary=False,
max_reads=None,
sample_reads=None):
t0 = time.time()
searchRegions = variant.searchRegions(searchDistance)
# This cludge tries the chromosomes as given ('chr4' or '4') and if that doesn't work
# tries to switch to the other variation ('4' or 'chr4')
try:
reads, supplementaryAlignmentsFound = _getreads(
searchRegions, bam, minmapq, pair_minmapq, single_ended,
include_supplementary, max_reads, sample_reads)
except ValueError as e:
oldchrom = searchRegions[0].chr()
try:
if "chr" in oldchrom:
newchrom = oldchrom.replace("chr", "")
searchRegions = [
Locus(l.chr().replace("chr", ""), l.start(), l.end(),
l.strand()) for l in searchRegions
]
else:
newchrom = "chr{}".format(oldchrom)
searchRegions = [
Locus("chr{}".format(l.chr()), l.start(), l.end(),
l.strand()) for l in searchRegions
]
logging.warn(
" Couldn't find reads on chromosome '{}'; trying instead '{}'"
.format(oldchrom, newchrom))
reads, supplementaryAlignmentsFound = _getreads(
searchRegions, bam, minmapq, pair_minmapq, single_ended,
include_supplementary, max_reads, sample_reads)
except ValueError:
raise e
t1 = time.time()
if supplementaryAlignmentsFound:
logging.warn(
" ** Supplementary alignments found: these alignments (with sam flag 0x800) **\n"
" ** are poorly documented among mapping software and may result in missing **\n"
" ** portions of reads; consider using the --include-supplementary **\n"
" ** command line argument if you think this is happening **"
)
logging.debug(" time to find reads and mates:{:.1f}s".format(t1 - t0))
logging.info(" number of reads found: {}".format(len(reads)))
return reads
def searchRegions(self, searchDistance):
chrom = self.chrom()
if len(self.region) < 2*searchDistance:
# return a single region
return [Locus(chrom, nonNegative(self.region.start()-searchDistance), self.region.end()+searchDistance, "+")]
else:
# return two regions, each around one of the ends of the inversion
searchRegions = []
searchRegions.append(Locus(chrom, nonNegative(self.region.start()-searchDistance),
self.region.start()+searchDistance, "+"))
searchRegions.append(Locus(chrom, nonNegative(self.region.end()-searchDistance),
self.region.end()+searchDistance, "+"))
return searchRegions
def searchRegions(self, searchDistance):
chrom = self.breakpoints[0].chr()
deletionRegion = Locus(chrom,
self.breakpoints[0].start() - searchDistance,
self.breakpoints[-1].end() + searchDistance,
"+")
return [deletionRegion]
def searchRegions(self, searchDistance):
searchRegions = []
for breakpoint in self.breakpoints:
searchRegions.append(Locus(breakpoint.chr(), nonNegative(breakpoint.start()-searchDistance),
breakpoint.end()+searchDistance, breakpoint.strand()))
return searchRegions
def getReads(variant,
bam,
minmapq,
pair_minmapq,
searchDistance,
single_ended=False,
include_supplementary=False):
t0 = time.time()
searchRegions = variant.searchRegions(searchDistance)
# This cludge tries the chromosomes as given ('chr4' or '4') and if that doesn't work
# tries to switch to the other variation ('4' or 'chr4')
try:
reads, supplementaryAlignmentsFound = _getreads(
searchRegions, bam, minmapq, pair_minmapq, single_ended,
include_supplementary)
except ValueError, e:
oldchrom = searchRegions[0].chr()
try:
if "chr" in oldchrom:
newchrom = oldchrom.replace("chr", "")
searchRegions = [
Locus(l.chr().replace("chr", ""), l.start(), l.end(),
l.strand()) for l in searchRegions
]
else:
newchrom = "chr{}".format(oldchrom)
searchRegions = [
Locus("chr{}".format(l.chr()), l.start(), l.end(),
l.strand()) for l in searchRegions
]
logging.warn(
" Couldn't find reads on chromosome '{}'; trying instead '{}'"
.format(oldchrom, newchrom))
reads, supplementaryAlignmentsFound = _getreads(
searchRegions, bam, minmapq, pair_minmapq, single_ended,
include_supplementary)
except ValueError:
raise e
def chromParts(self, allele):
b1 = self.breakpoints[0]
b2 = self.breakpoints[1]
segments = []
for i, breakpoint in enumerate(self.breakpoints):
segments.append(
Segment(breakpoint.chr(),
breakpoint.start() - self.alignDistance,
breakpoint.start() - 1, "+", 0 + i * 2))
segments.append(
Segment(breakpoint.chr(), breakpoint.start(),
breakpoint.start() + self.alignDistance, "+",
1 + i * 2))
# assert breakpoint.strand() == "+", breakpoint
# TODO: disambiguate reads mapping to multiple parts with the same alignment scores
# but different orientations
loci = [Locus(s.chrom, s.start, s.end, "+") for s in segments]
for i in range(len(loci) - 1):
for j in range(i + 1, len(loci)):
if loci[i].overlaps(loci[j]):
raise Exception(
"Not yet implemented - breakend-breakpoints near one another"
)
parts = []
if allele in ["ref", "amb"]:
name = "ref_{}".format(b1.chr())
parts.append(
ChromPart(name, [segments[0], segments[1]], self.sources))
name = "ref_{}".format(b2.chr())
if b1.chr() == b2.chr(): name += "b"
parts.append(
ChromPart(name, [segments[2], segments[3]], self.sources))
else:
if b1.strand() == "+": s1 = segments[0]
else: s1 = segments[1].antisense()
if b2.strand() == "+": s2 = segments[3]
else: s2 = segments[2].antisense()
name = "alt_{}/{}".format(b1.chr(), b2.chr())
parts.append(ChromPart(name, [s1, s2], self.sources))
return ChromPartsCollection(parts)
def getVariant(dataHub):
if dataHub.args.type.lower().startswith("del"):
assert len(dataHub.args.breakpoints) == 3, getBreakpointFormatsStr("del")
chrom = dataHub.args.breakpoints[0]
start = int(dataHub.args.breakpoints[1])
end = int(dataHub.args.breakpoints[2])
assert start < end
variant = Deletion.from_breakpoints(chrom, start-1, end-1, dataHub.alignDistance, dataHub.genome)
elif dataHub.args.type.lower() in ["ldel", "largedeletion"]:
assert len(dataHub.args.breakpoints) == 3, getBreakpointFormatsStr("ldel")
chrom = dataHub.args.breakpoints[0]
start = int(dataHub.args.breakpoints[1])
end = int(dataHub.args.breakpoints[2])
assert start < end
variant = LargeDeletion.from_breakpoints(chrom, start-1, end-1, dataHub.alignDistance, dataHub.genome)
elif dataHub.args.type.lower().startswith("ins"):
assert len(dataHub.args.breakpoints) in [3,4], getBreakpointFormatsStr("ins")
chrom = dataHub.args.breakpoints[0]
pos = int(dataHub.args.breakpoints[1])
if len(dataHub.args.breakpoints) == 3:
seq = dataHub.args.breakpoints[2]
end = pos
else:
end = int(dataHub.args.breakpoints[2])
seq = dataHub.args.breakpoints[3]
variant = Insertion(Locus(chrom, pos, end, "+"), seq, dataHub.alignDistance, dataHub.genome)
elif dataHub.args.type.lower().startswith("inv"):
assert len(dataHub.args.breakpoints) == 3, getBreakpointFormatsStr("inv")
chrom = dataHub.args.breakpoints[0]
start = int(dataHub.args.breakpoints[1])
end = int(dataHub.args.breakpoints[2])
if dataHub.args.min_mapq is None:
dataHub.args.min_mapq = -1
variant = Inversion(Locus(chrom, start, end, "+"), dataHub.alignDistance, dataHub.genome)
elif dataHub.args.type.lower().startswith("mei"):
assert len(dataHub.args.breakpoints) >= 4, getBreakpointFormatsStr("mei")
insertionBreakpoint = Locus(dataHub.args.breakpoints[1], dataHub.args.breakpoints[2], dataHub.args.breakpoints[2], "+")
meName = dataHub.args.breakpoints[3]
meStrand = getListDefault(dataHub.args.breakpoints, 4, "+")
meStart = getListDefault(dataHub.args.breakpoints, 5, 0)
meEnd = getListDefault(dataHub.args.breakpoints, 6, 1e100)
meCoords = Locus(meName, meStart, meEnd, meStrand)
meFasta = genomesource.FastaGenomeSource(dataHub.args.breakpoints[0])
variant = MobileElementInsertion(insertionBreakpoint, meCoords, meFasta, dataHub.alignDistance, dataHub.genome)
elif dataHub.args.type.lower().startswith("tra"):
assert len(dataHub.args.breakpoints) == 5, getBreakpointFormatsStr("tra")
chrom1 = dataHub.args.breakpoints[0]
start1 = int(dataHub.args.breakpoints[1])
chrom2 = dataHub.args.breakpoints[2]
start2 = int(dataHub.args.breakpoints[3])
orientation = dataHub.args.breakpoints[4]
if dataHub.args.min_mapq is None:
dataHub.args.min_mapq = -1
variant = Translocation(Locus(chrom1, start1, start1, "+"),
Locus(chrom2, start2, start2, orientation),
dataHub.alignDistance, dataHub.genome)
elif dataHub.args.type.lower() in ["bkend", "breakend"]:
assert len(dataHub.args.breakpoints) == 6, getBreakpointFormatsStr("bkend")
chrom1 = dataHub.args.breakpoints[0]
start1 = int(dataHub.args.breakpoints[1])
strand1 = dataHub.args.breakpoints[2]
chrom2 = dataHub.args.breakpoints[3]
start2 = int(dataHub.args.breakpoints[4])
strand2 = dataHub.args.breakpoints[5]
if dataHub.args.min_mapq is None:
dataHub.args.min_mapq = -1
variant = Breakend(Locus(chrom1, start1, start1, strand1),
Locus(chrom2, start2, start2, strand2),
dataHub.alignDistance, dataHub.genome)
else:
raise Exception("only accept event types of deletion, insertion, mei, translocation or breakend")
logging.info(" Variant: {}".format(variant))
return variant
def from_breakpoints(class_, chrom, first, second, alignDistance, fasta):
breakpoint1 = Locus(chrom, first, first, "+")
breakpoint2 = Locus(chrom, second, second, "+")
return class_(breakpoint1, breakpoint2, alignDistance, fasta)
def searchRegions(self, searchDistance):
chrom = self.breakpoints[0].chr()
return [Locus(chrom, nonNegative(self.breakpoints[0].start()-searchDistance),
self.breakpoints[-1].end()+searchDistance, "+")]
def from_breakpoints(class_, chrom, first, second, alignDistance, fasta):
breakpointLoci = [Locus(chrom, first, first, "+"), Locus(chrom, second, second, "+")]
return class_(breakpointLoci, alignDistance, fasta)
