def test_readsToWiggle_pysam(self):
reads = pysam.Samfile(os.path.join(clipper.test_dir(), "allup_test.bam"))
reads = reads.fetch(region="chr15:91536649-91537641")
wiggle, jxns, pos_counts, lengths, allreads = readsToWiggle_pysam(reads, 91537632, 91537675, '-', 'center', False)
#wiggle, pos_counts, lengths = readsToWiggle_pysam(reads, 91537632, 91537675, '-', 'center', False)
wiggle_true = [ 2. , 2., 2. , 2. , 2. , 2. , 2. , 2. , 11. , 11., 11. , 11. ,11. , 11. , 11.,
11. , 11., 11., 11. , 11. ,11. , 11. , 11. , 11., 11. , 11. , 11. ,11. , 11. ,11.,
11. , 11., 11., 9. , 9. , 9. , 9. , 9., 9. , 9., 9. , 0. , 0., 0.]
print wiggle
for true, test in zip(wiggle_true, wiggle):
self.assertEqual(test, true)
#
pos_counts_true = [ 0. , 0., 0. , 0. ,0. , 0., 0., 0., 0., 0., 0., 0., 0. , 0. ,
0. , 0. , 2., 0., 0. , 0., 0., 0., 0. , 0., 9., 0. , 0., 0. , 0. ,
0. , 0. , 0. , 0. , 0., 0., 0., 0. , 0., 0. , 0. , 0., 0., 0. , 0.]
for true, test in zip(pos_counts_true, pos_counts):
self.assertEqual(test, true)
assert lengths == [33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33]
reads = pysam.Samfile(os.path.join(clipper.test_dir(), "allup_test.bam"))
reads = reads.fetch(region="chr15:91536649-91537641")
wiggle, jxns, pos_counts, lengths, allreads = readsToWiggle_pysam(reads, 91537632, 91537675, '-', 'center', True)
#wiggle, pos_counts, lengths = readsToWiggle_pysam(reads, 91537632, 91537675, '-', 'center', True)
wiggle_true = [0.06060606060606061, 0.06060606060606061, 0.06060606060606061, 0.06060606060606061, 0.06060606060606061, 0.06060606060606061, 0.06060606060606061, 0.06060606060606061, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.2727272727272727, 0.2727272727272727, 0.2727272727272727, 0.2727272727272727, 0.2727272727272727, 0.2727272727272727, 0.2727272727272727, 0.2727272727272727, 0.0, 0.0, 0.0]
for true, test in zip(wiggle_true, wiggle):
self.assertEqual(test, true)
def test_readsToWiggle_pysam(self):
reads = pysam.Samfile(
os.path.join(clipper.test_dir(), "allup_test.bam"))
reads = reads.fetch(region="chr15:91536649-91537641")
wiggle, jxns, pos_counts, lengths, allreads = readsToWiggle_pysam(
reads, 91537632, 91537675, '-', 'center', False)
#wiggle, pos_counts, lengths = readsToWiggle_pysam(reads, 91537632, 91537675, '-', 'center', False)
wiggle_true = [
2., 2., 2., 2., 2., 2., 2., 2., 11., 11., 11., 11., 11., 11., 11.,
11., 11., 11., 11., 11., 11., 11., 11., 11., 11., 11., 11., 11.,
11., 11., 11., 11., 11., 9., 9., 9., 9., 9., 9., 9., 9., 0., 0., 0.
]
print wiggle
for true, test in zip(wiggle_true, wiggle):
self.assertEqual(test, true)
#
pos_counts_true = [
0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 2.,
0., 0., 0., 0., 0., 0., 0., 9., 0., 0., 0., 0., 0., 0., 0., 0., 0.,
0., 0., 0., 0., 0., 0., 0., 0., 0., 0.
]
for true, test in zip(pos_counts_true, pos_counts):
self.assertEqual(test, true)
assert lengths == [33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33]
reads = pysam.Samfile(
os.path.join(clipper.test_dir(), "allup_test.bam"))
reads = reads.fetch(region="chr15:91536649-91537641")
wiggle, jxns, pos_counts, lengths, allreads = readsToWiggle_pysam(
reads, 91537632, 91537675, '-', 'center', True)
#wiggle, pos_counts, lengths = readsToWiggle_pysam(reads, 91537632, 91537675, '-', 'center', True)
wiggle_true = [
0.06060606060606061, 0.06060606060606061, 0.06060606060606061,
0.06060606060606061, 0.06060606060606061, 0.06060606060606061,
0.06060606060606061, 0.06060606060606061, 0.33333333333333326,
0.33333333333333326, 0.33333333333333326, 0.33333333333333326,
0.33333333333333326, 0.33333333333333326, 0.33333333333333326,
0.33333333333333326, 0.33333333333333326, 0.33333333333333326,
0.33333333333333326, 0.33333333333333326, 0.33333333333333326,
0.33333333333333326, 0.33333333333333326, 0.33333333333333326,
0.33333333333333326, 0.33333333333333326, 0.33333333333333326,
0.33333333333333326, 0.33333333333333326, 0.33333333333333326,
0.33333333333333326, 0.33333333333333326, 0.33333333333333326,
0.2727272727272727, 0.2727272727272727, 0.2727272727272727,
0.2727272727272727, 0.2727272727272727, 0.2727272727272727,
0.2727272727272727, 0.2727272727272727, 0.0, 0.0, 0.0
]
for true, test in zip(wiggle_true, wiggle):
self.assertEqual(test, true)
def call_peaks(loc, gene_length, bam_fileobj=None, bam_file=None,
margin=25, fdr_alpha=0.05, user_threshold=None,
minreads=20, poisson_cutoff=0.05,
plotit=False, w_cutoff=10, windowsize=1000,
SloP=False, correct_p=False):
"""
calls peaks for an individual gene
loc - string of all gene location
gene_length - effective length of gene
takes bam file or bam file object. Serial uses object parallel uses location (name)
margin - space between sections for calling new peaks
fdr_alpha - false discovery rate, p-value bonferoni correct from peaks script (called in setup)
user_threshold - user defined FDR thershold (probably should be factored into fdr_alpha
minreads - min reads in section to try and call peaks
poisson_cutoff - p-value for signifance cut off for number of reads in peak that gets called - might want to use ashifted distribution
plotit - makes figures
w_cutoff - width cutoff, peaks narrower than this are discarted
windowssize - for super local calculation distance left and right to look
SloP - super local p-value instead of gene-wide p-value
correct_p - boolean bonferoni correction of p-values from poisson
"""
#setup
chrom, gene_name, tx_start, tx_end, signstrand = loc
#logic reading bam files
if bam_file is None and bam_fileobj is None:
#using a file opbject is faster for serial processing
#but doesn't work in parallel
verboseprint("""you have to pick either bam file or bam file
object, not both""")
exit()
elif bam_fileobj is None:
bam_fileobj = pysam.Samfile(bam_file, 'rb')
tx_start, tx_end = [int(x) for x in [tx_start, tx_end]]
subset_reads = bam_fileobj.fetch(reference=chrom, start=tx_start, end=tx_end)
#need to document reads to wiggle
wiggle, jxns, pos_counts, lengths, allreads = readsToWiggle_pysam(subset_reads, tx_start, tx_end, signstrand, "center", False)
#wiggle, pos_counts, lengths = readsToWiggle_pysam(subset_reads, tx_start, tx_end, signstrand, "center", False)
#TODO have a check to kill this if there aren't any reads in a region
result = peaks_from_info(list(wiggle), pos_counts, lengths, loc, gene_length, margin, fdr_alpha, user_threshold, minreads, poisson_cutoff, plotit, w_cutoff, windowsize, SloP, correct_p)
return result
def assign_reads(gene, splicedict=None, bam_file=None,
alignment_slop=10, flip=True, splicetypes=None):
if splicedict is None or bam_file is None:
raise Exception
bam_fileobj = pysam.Samfile(bam_file, 'rb')
data = {}
chrom = splicedict["chromosome"]
strand = splicedict["strand"]
tx_start = splicedict["tx_start"]
tx_end = splicedict["tx_end"]
signstrand = None
if flip is True:
usestrand = strand * -1
else:
usestrand = strand
if usestrand == 1:
signstrand = "+"
elif usestrand == -1:
signstrand = "-"
interval = pybedtools.Interval(chrom, tx_start, tx_end, strand=signstrand)
subset_reads = bam_fileobj.fetch(reference=chrom, start=tx_start,end=tx_end)
(wig, jxns, nrCounts, readLengths,
reads) = readsToWiggle_pysam(subset_reads, (tx_start-1000),
(tx_end+1000), signstrand, "center", False)
data["descriptor"] = gene
if "SE" in splicedict and "SE" in splicetypes:
data["SE"] = {}
for loc in splicedict["SE"]:
#rangestart = splicedict[gene]["SE"][loc]["rangestart"]
#rangeend = splicedict[gene]["SE"][loc]["rangeend"]
data["SE"][loc] = {}
data["SE"][loc]["IN"] = 0
data["SE"][loc]["EX"] = 0
bodyLoc = splicedict['SE'][loc]["BODY"]
upLoc = splicedict['SE'][loc]["UP"]
downLoc = splicedict['SE'][loc]["DOWN"]
if strand == 1:
upIntronLoc = upLoc.split("-")[1] + "-" + bodyLoc.split("-")[0]
downIntronLoc = bodyLoc.split("-")[1] + "-" + downLoc.split("-")[0]
else:
upIntronLoc = bodyLoc.split("-")[1] + "-" + upLoc.split("-")[0]
downIntronLoc = downLoc.split("-")[1] + "-" + bodyLoc.split("-")[0]
try:
data["SE"][loc]["BODY_RPK"] = region_rpk(pybedtools.Interval(chrom, *map(int, bodyLoc.split("-")), strand=signstrand), bam_fileobj)
data["SE"][loc]["UP_RPK"] = region_rpk(pybedtools.Interval(chrom, *map(int, upLoc.split("-")), strand=signstrand), bam_fileobj)
data["SE"][loc]["DOWN_RPK"] = region_rpk(pybedtools.Interval(chrom, *map(int, downLoc.split("-")), strand=signstrand), bam_fileobj)
data["SE"][loc]["UPI_RPK"] = region_rpk(pybedtools.Interval(chrom, *map(int, upIntronLoc.split("-")), strand=signstrand), bam_fileobj)
data["SE"][loc]["DOWNI_RPK"] = region_rpk(pybedtools.Interval(chrom, *map(int, downIntronLoc.split("-")), strand=signstrand), bam_fileobj)
except:
#import pdb; pdb.set_trace()
print "uh oh %s" %(gene + loc)
continue
for structure in splicedict["SE"][loc]["IN"]:
if structure.startswith("j"):
structurestrip = structure.lstrip("j")
structurestrip = tuple(map(int, structurestrip.split(":")))
if structurestrip in jxns:
data["SE"][loc]["IN"] += jxns[structurestrip]
for structure in splicedict["SE"][loc]["EX"]:
if structure.startswith("j"):
structurestrip = structure.lstrip("j")
structurestrip = tuple(map(int, structurestrip.split(":")))
if structurestrip in jxns:
data["SE"][loc]["EX"] += jxns[structurestrip]
if "MXE" in splicedict and "MXE" in splicetypes:
data["MXE"] = {}
# for loc in splicedict[gene]["MXE"]:
for loc in splicedict["MXE"]:
#rangestart = splicedict[gene]["SE"][loc]["rangestart"]
#rangeend = splicedict[gene]["SE"][loc]["rangeend"]
data["MXE"][loc] = {}
data["MXE"][loc]["A"] = 0
data["MXE"][loc]["B"] = 0
#import code
#code.interact(local=locals())
for structure in splicedict["MXE"][loc]["A"]:
if structure.startswith("j"):
structurestrip = structure.lstrip("j")
structurestrip = tuple(map(int, structurestrip.split(":")))
if structurestrip in jxns:
data["MXE"][loc]["A"] += jxns[structurestrip]
elif structure.startswith("b"):
continue
exstart, exstop = map(int, structure.lstrip("b").split("-"))
for position in range(exstart, (exstop+1)):
if position in reads:
for read_end in reads[position]:
if read_end <= exstop:
data["MXE"][loc]["A"] += reads[position][read_end]
for structure in splicedict["MXE"][loc]["B"]:
if structure.startswith("j"):
structurestrip = structure.lstrip("j")
structurestrip = tuple(map(int, structurestrip.split(":")))
if structurestrip in jxns:
data["MXE"][loc]["B"] += jxns[structurestrip]
elif structure.startswith("b"):
continue
exstart, exstop = map(int, structure.lstrip("b").split("-"))
for position in range(exstart, (exstop+1)):
if position in reads:
for read_end in reads[position]:
if read_end <= exstop:
data["MXE"][loc]["B"] += reads[position][read_end]
return data
def assign_reads(gene, splicedict=None, bam_file=None, alignment_slop=10, flip=True, splicetypes=None):
if splicedict is None or bam_file is None:
raise Exception
bam_fileobj = pysam.Samfile(bam_file, 'rb')
data = {}
chrom = splicedict["chromosome"]
strand = splicedict["strand"]
tx_start = splicedict["tx_start"]
tx_end = splicedict["tx_end"]
signstrand = None
if flip is not None:
if flip is True:
usestrand = strand * -1
else:
usestrand = strand
if usestrand == 1:
signstrand = "+"
elif usestrand == -1:
signstrand = "-"
subset_reads = bam_fileobj.fetch(reference=chrom, start=tx_start,end=tx_end)
wig, jxns, nrCounts, readLengths, reads = readsToWiggle_pysam(subset_reads, (tx_start-1000), (tx_end+1000), signstrand, "center", False)
data["descriptor"] = gene
if "SE" in splicedict and "SE" in splicetypes:
data["SE"] = {}
for loc in splicedict["SE"]:
#rangestart = splicedict[gene]["SE"][loc]["rangestart"]
#rangeend = splicedict[gene]["SE"][loc]["rangeend"]
data["SE"][loc] = {}
data["SE"][loc]["IN"] = 0
data["SE"][loc]["EX"] = 0
for structure in splicedict["SE"][loc]["IN"]:
if structure.startswith("j"):
structurestrip = structure.lstrip("j")
structurestrip = tuple(map(int, structurestrip.split(":")))
if structurestrip in jxns:
data["SE"][loc]["IN"] += jxns[structurestrip]
elif structure.startswith("b"):
continue #skip exon body
exstart, exstop = map(int, structure.lstrip("b").split("-"))
for position in range(exstart, (exstop+1)):
if position in reads:
for read_end in reads[position]:
if read_end <= exstop:
data["SE"][loc]["IN"] += reads[position][read_end]
#for. read in reads:
# rstart, rstop = map(int, read.split("-"))
# if rstart >= (exstart-alignment_slop) and rstop <= (exstop + alignment_slop):
# data["SE"][loc]["IN"] += reads[read]
# else:
# pass
for structure in splicedict["SE"][loc]["EX"]:
if structure.startswith("j"):
structurestrip = structure.lstrip("j")
structurestrip = tuple(map(int, structurestrip.split(":")))
if structurestrip in jxns:
data["SE"][loc]["EX"] += jxns[structurestrip]
if "MXE" in splicedict and "MXE" in splicetypes:
data["MXE"] = {}
# for loc in splicedict[gene]["MXE"]:
for loc in splicedict["MXE"]:
#rangestart = splicedict[gene]["SE"][loc]["rangestart"]
#rangeend = splicedict[gene]["SE"][loc]["rangeend"]
data["MXE"][loc] = {}
data["MXE"][loc]["A"] = 0
data["MXE"][loc]["B"] = 0
#import code
#code.interact(local=locals())
for structure in splicedict["MXE"][loc]["A"]:
if structure.startswith("j"):
structurestrip = structure.lstrip("j")
structurestrip = tuple(map(int, structurestrip.split(":")))
if structurestrip in jxns:
data["MXE"][loc]["A"] += jxns[structurestrip]
elif structure.startswith("b"):
continue
exstart, exstop = map(int, structure.lstrip("b").split("-"))
for position in range(exstart, (exstop+1)):
if position in reads:
for read_end in reads[position]:
if read_end <= exstop:
data["MXE"][loc]["A"] += reads[position][read_end]
for structure in splicedict["MXE"][loc]["B"]:
if structure.startswith("j"):
structurestrip = structure.lstrip("j")
structurestrip = tuple(map(int, structurestrip.split(":")))
if structurestrip in jxns:
data["MXE"][loc]["B"] += jxns[structurestrip]
elif structure.startswith("b"):
continue
exstart, exstop = map(int, structure.lstrip("b").split("-"))
for position in range(exstart, (exstop+1)):
if position in reads:
for read_end in reads[position]:
if read_end <= exstop:
data["MXE"][loc]["B"] += reads[position][read_end]
return data
def call_peaks(loc,
gene_length,
bam_fileobj=None,
bam_file=None,
margin=25,
fdr_alpha=0.05,
user_threshold=None,
minreads=20,
poisson_cutoff=0.05,
plotit=False,
w_cutoff=10,
windowsize=1000,
SloP=False,
correct_p=False):
"""
calls peaks for an individual gene
loc - string of all gene location
gene_length - effective length of gene
takes bam file or bam file object. Serial uses object parallel uses location (name)
margin - space between sections for calling new peaks
fdr_alpha - false discovery rate, p-value bonferoni correct from peaks script (called in setup)
user_threshold - user defined FDR thershold (probably should be factored into fdr_alpha
minreads - min reads in section to try and call peaks
poisson_cutoff - p-value for signifance cut off for number of reads in peak that gets called - might want to use ashifted distribution
plotit - makes figures
w_cutoff - width cutoff, peaks narrower than this are discarted
windowssize - for super local calculation distance left and right to look
SloP - super local p-value instead of gene-wide p-value
correct_p - boolean bonferoni correction of p-values from poisson
"""
#setup
chrom, gene_name, tx_start, tx_end, signstrand = loc
#logic reading bam files
if bam_file is None and bam_fileobj is None:
#using a file opbject is faster for serial processing
#but doesn't work in parallel
verboseprint("""you have to pick either bam file or bam file
object, not both""")
exit()
elif bam_fileobj is None:
bam_fileobj = pysam.Samfile(bam_file, 'rb')
tx_start, tx_end = [int(x) for x in [tx_start, tx_end]]
subset_reads = bam_fileobj.fetch(reference=chrom,
start=tx_start,
end=tx_end)
#need to document reads to wiggle
wiggle, jxns, pos_counts, lengths, allreads = readsToWiggle_pysam(
subset_reads, tx_start, tx_end, signstrand, "center", False)
#wiggle, pos_counts, lengths = readsToWiggle_pysam(subset_reads, tx_start, tx_end, signstrand, "center", False)
#TODO have a check to kill this if there aren't any reads in a region
result = peaks_from_info(list(wiggle), pos_counts, lengths, loc,
gene_length, margin, fdr_alpha, user_threshold,
minreads, poisson_cutoff, plotit, w_cutoff,
windowsize, SloP, correct_p)
return result
def assign_reads(gene,
splicedict=None,
bam_file=None,
alignment_slop=10,
flip=True,
splicetypes=None):
if splicedict is None or bam_file is None:
raise Exception
bam_fileobj = pysam.Samfile(bam_file, 'rb')
data = {}
chrom = splicedict["chromosome"]
strand = splicedict["strand"]
tx_start = splicedict["tx_start"]
tx_end = splicedict["tx_end"]
signstrand = None
if flip is True:
usestrand = strand * -1
else:
usestrand = strand
if usestrand == 1:
signstrand = "+"
elif usestrand == -1:
signstrand = "-"
interval = pybedtools.Interval(chrom, tx_start, tx_end, strand=signstrand)
subset_reads = bam_fileobj.fetch(reference=chrom,
start=tx_start,
end=tx_end)
(wig, jxns, nrCounts, readLengths,
reads) = readsToWiggle_pysam(subset_reads, (tx_start - 1000),
(tx_end + 1000), signstrand, "center", False)
data["descriptor"] = gene
if "SE" in splicedict and "SE" in splicetypes:
data["SE"] = {}
for loc in splicedict["SE"]:
#rangestart = splicedict[gene]["SE"][loc]["rangestart"]
#rangeend = splicedict[gene]["SE"][loc]["rangeend"]
data["SE"][loc] = {}
data["SE"][loc]["IN"] = 0
data["SE"][loc]["EX"] = 0
bodyLoc = splicedict['SE'][loc]["BODY"]
upLoc = splicedict['SE'][loc]["UP"]
downLoc = splicedict['SE'][loc]["DOWN"]
if strand == 1:
upIntronLoc = upLoc.split("-")[1] + "-" + bodyLoc.split("-")[0]
downIntronLoc = bodyLoc.split("-")[1] + "-" + downLoc.split(
"-")[0]
else:
upIntronLoc = bodyLoc.split("-")[1] + "-" + upLoc.split("-")[0]
downIntronLoc = downLoc.split("-")[1] + "-" + bodyLoc.split(
"-")[0]
try:
data["SE"][loc]["BODY_RPK"] = region_rpk(
pybedtools.Interval(chrom,
*map(int, bodyLoc.split("-")),
strand=signstrand), bam_fileobj)
data["SE"][loc]["UP_RPK"] = region_rpk(
pybedtools.Interval(chrom,
*map(int, upLoc.split("-")),
strand=signstrand), bam_fileobj)
data["SE"][loc]["DOWN_RPK"] = region_rpk(
pybedtools.Interval(chrom,
*map(int, downLoc.split("-")),
strand=signstrand), bam_fileobj)
data["SE"][loc]["UPI_RPK"] = region_rpk(
pybedtools.Interval(chrom,
*map(int, upIntronLoc.split("-")),
strand=signstrand), bam_fileobj)
data["SE"][loc]["DOWNI_RPK"] = region_rpk(
pybedtools.Interval(chrom,
*map(int, downIntronLoc.split("-")),
strand=signstrand), bam_fileobj)
except:
#import pdb; pdb.set_trace()
print "uh oh %s" % (gene + loc)
continue
for structure in splicedict["SE"][loc]["IN"]:
if structure.startswith("j"):
structurestrip = structure.lstrip("j")
structurestrip = tuple(map(int, structurestrip.split(":")))
if structurestrip in jxns:
data["SE"][loc]["IN"] += jxns[structurestrip]
for structure in splicedict["SE"][loc]["EX"]:
if structure.startswith("j"):
structurestrip = structure.lstrip("j")
structurestrip = tuple(map(int, structurestrip.split(":")))
if structurestrip in jxns:
data["SE"][loc]["EX"] += jxns[structurestrip]
if "MXE" in splicedict and "MXE" in splicetypes:
data["MXE"] = {}
# for loc in splicedict[gene]["MXE"]:
for loc in splicedict["MXE"]:
#rangestart = splicedict[gene]["SE"][loc]["rangestart"]
#rangeend = splicedict[gene]["SE"][loc]["rangeend"]
data["MXE"][loc] = {}
data["MXE"][loc]["A"] = 0
data["MXE"][loc]["B"] = 0
#import code
#code.interact(local=locals())
for structure in splicedict["MXE"][loc]["A"]:
if structure.startswith("j"):
structurestrip = structure.lstrip("j")
structurestrip = tuple(map(int, structurestrip.split(":")))
if structurestrip in jxns:
data["MXE"][loc]["A"] += jxns[structurestrip]
elif structure.startswith("b"):
continue
exstart, exstop = map(int,
structure.lstrip("b").split("-"))
for position in range(exstart, (exstop + 1)):
if position in reads:
for read_end in reads[position]:
if read_end <= exstop:
data["MXE"][loc]["A"] += reads[position][
read_end]
for structure in splicedict["MXE"][loc]["B"]:
if structure.startswith("j"):
structurestrip = structure.lstrip("j")
structurestrip = tuple(map(int, structurestrip.split(":")))
if structurestrip in jxns:
data["MXE"][loc]["B"] += jxns[structurestrip]
elif structure.startswith("b"):
continue
exstart, exstop = map(int,
structure.lstrip("b").split("-"))
for position in range(exstart, (exstop + 1)):
if position in reads:
for read_end in reads[position]:
if read_end <= exstop:
data["MXE"][loc]["B"] += reads[position][
read_end]
return data
