def get_seq(self, chrom, start, end, strand):
chrom = match_chrom_format(chrom, self.keys())
# seq = self.fasta[chrom][start:end+1]
seq = self.fasta.fetch(chrom, start, end + 1)
if strand == "-":
seq = reverse_comp(seq)
return seq
def get_seq(self, chrom, start, end, strand):
chrom = match_chrom_format(chrom, self.keys())
# seq = self.fasta[chrom][start:end+1]
seq = self.fasta.fetch(chrom, start, end+1)
if strand == "-":
seq = reverse_comp(seq)
return seq
def fetch_from_tabix(path, chrom, start, end):
import pysam
bed = pysam.TabixFile(path)
chrom = match_chrom_format(chrom, bed.contigs)
for locus in bed.fetch(chrom, start, end):
locus = locus.split()
yield tx_from_bedfields(locus)
def fetch_from_tabix(path, chrom, start, end):
import pysam
bed = pysam.TabixFile(path)
chrom = match_chrom_format(chrom, bed.contigs)
for locus in bed.fetch(chrom, start, end):
locus = locus.split()
yield tx_from_bedfields(locus)
def fetch_from_bigbed(path, chrom, start, end):
import pyBigWig
bed = pyBigWig.open(path)
assert bed.isBigBed(), "Oops, for some reason I was expecting a bed file: {}".format(path)
chrom = match_chrom_format(chrom, bed.chroms().keys())
for cur_start, cur_end, bed_line in bed.entries(chrom, start, end):
bed_line = bed_line.split()
yield tx_from_bedfields([chrom, cur_start, cur_end] + bed_line)
def fetch_from_bigbed(path, chrom, start, end):
import pyBigWig
bed = pyBigWig.open(path)
assert bed.isBigBed(
), "Oops, for some reason I was expecting a bed file: {}".format(path)
chrom = match_chrom_format(chrom, bed.chroms().keys())
for cur_start, cur_end, bed_line in bed.entries(chrom, start, end):
bed_line = bed_line.split()
yield tx_from_bedfields([chrom, cur_start, cur_end] + bed_line)
def tally_reads(self, bam):
depths = []
for pileupcolumn in bam.pileup(match_chrom_format(self.chrom, bam.references), self.start, self.end, truncate=True):
depths.append(pileupcolumn.n)
for pileupread in pileupcolumn.pileups:
if pileupread.is_refskip:
continue
elif pileupread.is_del:
self.add_count(pileupcolumn.pos, "DEL")
else:
nuc = pileupread.alignment.query_sequence[pileupread.query_position]
if nuc != "N":
self.add_count(pileupcolumn.pos, nuc)
if pileupread.indel > 0:
self.add_count(pileupcolumn.pos, "INS")
def layout(self, scale):
super().layout(scale)
x = []
y = []
binsize = max(1, int((scale.end-scale.start) / self.nbins))
chrom = match_chrom_format(scale.chrom, self.bigwig.chroms().keys())
for i in range(scale.start, scale.end, binsize):
values = self.bigwig.stats(chrom, i, i+binsize)
x.append(i+binsize/2)
y.append(values[0])
self.series = {"vals":Series(x, y, color="black")}
self.min_y = min(y)
self.max_y = max(y)
def layout(self, scale):
super().layout(scale)
x = []
y = []
binsize = max(1, int((scale.end-scale.start) / self.nbins))
chrom = match_chrom_format(scale.chrom, self.bigwig.chroms().keys())
for i in range(scale.start, scale.end, binsize):
values = self.bigwig.stats(chrom, i, i+binsize)
x.append(i+binsize/2)
y.append(values[0])
self.series = {"vals":Series(x, y, color="black")}
self.min_y = min(y)
self.max_y = max(y)
def layout(self, scale):
self.scale = scale
categories = set()
chrom = match_chrom_format(self.scale.chrom, self.bam.references)
for read in self.bam.fetch(chrom, self.scale.start, self.scale.end):
category = self.keyfn(read)
categories.add(category)
categories = sorted(categories)
self.height = 0
for category in categories:
cur_track = self.bam_track_class(self.bam_path, name=self.category_label_fn(category))
cur_track.include_read_fn = _get_filter_fn(self.keyfn, category)
cur_track.layout(scale)
self.height += cur_track.height + self.space_between
self.subtracks.append(cur_track)
def layout(self, scale):
self.scale = scale
categories = set()
chrom = match_chrom_format(self.scale.chrom, self.bam.references)
for read in self.bam.fetch(chrom, self.scale.start, self.scale.end):
category = self.keyfn(read)
categories.add(category)
categories = sorted(categories)
self.height = 0
for category in categories:
cur_track = self.bam_track_class(self.bam_path, name=self.category_label_fn(category))
cur_track.include_read_fn = _get_filter_fn(self.keyfn, category)
cur_track.layout(scale)
self.height += cur_track.height + self.space_between
self.subtracks.append(cur_track)
def tally_reads(self, bam):
depths = []
for pileupcolumn in bam.pileup(match_chrom_format(
self.chrom, bam.references),
self.start,
self.end,
truncate=True):
depths.append(pileupcolumn.n)
for pileupread in pileupcolumn.pileups:
if pileupread.is_refskip:
continue
elif pileupread.is_del:
self.add_count(pileupcolumn.pos, "DEL")
else:
nuc = pileupread.alignment.query_sequence[
pileupread.query_position]
if nuc != "N":
self.add_count(pileupcolumn.pos, nuc)
if pileupread.indel > 0:
self.add_count(pileupcolumn.pos, "INS")
def match_chrom_format(self, chrom):
"""
Ensures that the input argument `chrom` matches the chromosome name formatting in
the bam file being visualized (ie "chr14" vs "14").
"""
return match_chrom_format(chrom, self.bam.references)
def match_chrom_format(self, chrom):
"""
Ensures that the input argument `chrom` matches the chromosome name formatting in
the bam file being visualized (ie "chr14" vs "14").
"""
return match_chrom_format(chrom, self.bam.references)
def get_seq(self, chrom, start, end, strand):
chrom = match_chrom_format(chrom, self.keys())
seq = self.names_to_contigs[chrom][start:end + 1]
if strand == "-":
seq = reverse_comp(seq)
return seq
def get_seq(self, chrom, start, end, strand):
chrom = match_chrom_format(chrom, self.keys())
seq = self.names_to_contigs[chrom][start:end+1]
if strand == "-":
seq = reverse_comp(seq)
return seq