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import numpy as np
import multiprocessing
import time
from deeptools import countReadsPerBin
from deeptools.utilities import getTLen
from deeptoolsintervals import GTF
class SumCoveragePerBin(countReadsPerBin.CountReadsPerBin):
r"""This is an extension of CountReadsPerBin for use with plotFingerprint.
There, we need to sum the per-base coverage.
"""
def get_coverage_of_region(self, bamHandle, chrom, regions,
fragmentFromRead_func=None):
"""
Returns a numpy array that corresponds to the number of reads
that overlap with each tile.
>>> test = Tester()
>>> import pysam
>>> c = SumCoveragePerBin([], stepSize=1, extendReads=300)
For this case the reads are length 36. The number of overlapping
read fragments is 4 and 5 for the positions tested. Note that reads are
NOT extended, due to there being a 0 length input list of BAM files!
>>> c.get_coverage_of_region(pysam.AlignmentFile(test.bamFile_PE), 'chr2',
... [(5000833, 5000834), (5000834, 5000835)])
array([4., 5.])
In the following case the reads length is 50. Reads are not extended.
>>> c.extendReads=False
>>> c.get_coverage_of_region(pysam.AlignmentFile(test.bamFile2), '3R', [(148, 150), (150, 152), (152, 154)])
array([2., 4., 4.])
"""
if not fragmentFromRead_func:
fragmentFromRead_func = self.get_fragment_from_read
nbins = len(regions)
if len(regions[0]) == 3:
nbins = 0
for reg in regions:
nbins += (reg[1] - reg[0]) // reg[2]
coverages = np.zeros(nbins, dtype='float64')
if self.defaultFragmentLength == 'read length':
extension = 0
else:
extension = self.maxPairedFragmentLength
blackList = None
if self.blackListFileName is not None:
blackList = GTF(self.blackListFileName)
vector_start = 0
for idx, reg in enumerate(regions):
if len(reg) == 3:
tileSize = int(reg[2])
nRegBins = (reg[1] - reg[0]) // tileSize
else:
nRegBins = 1
tileSize = int(reg[1] - reg[0])
# Blacklisted regions have a coverage of 0
if blackList and blackList.findOverlaps(chrom, reg[0], reg[1]):
continue
regStart = int(max(0, reg[0] - extension))
regEnd = reg[1] + int(extension)
# If alignments are extended and there's a blacklist, ensure that no
# reads originating in a blacklist are fetched
if blackList and reg[0] > 0 and extension > 0:
o = blackList.findOverlaps(chrom, regStart, reg[0])
if o is not None and len(o) > 0:
regStart = o[-1][1]
o = blackList.findOverlaps(chrom, reg[1], regEnd)
if o is not None and len(o) > 0:
regEnd = o[0][0]
start_time = time.time()
# caching seems faster. TODO: profile the function
c = 0
try:
# BAM input
if chrom not in bamHandle.references:
raise NameError("chromosome {} not found in bam file".format(chrom))
except:
# bigWig input, as used by plotFingerprint
if bamHandle.chroms(chrom):
_ = np.array(bamHandle.stats(chrom, regStart, regEnd, type="mean", nBins=nRegBins), dtype=np.float)
_[np.isnan(_)] = 0.0
_ = _ * tileSize
coverages += _
continue
else:
raise NameError("chromosome {} not found in bigWig file with chroms {}".format(chrom, bamHandle.chroms()))
prev_pos = set()
lpos = None
# of previous processed read pair
for read in bamHandle.fetch(chrom, regStart, regEnd):
if read.is_unmapped:
continue
if self.minMappingQuality and read.mapq < self.minMappingQuality:
continue
# filter reads based on SAM flag
if self.samFlag_include and read.flag & self.samFlag_include != self.samFlag_include:
continue
if self.samFlag_exclude and read.flag & self.samFlag_exclude != 0:
continue
# Fragment lengths
tLen = getTLen(read)
if self.minFragmentLength > 0 and tLen < self.minFragmentLength:
continue
if self.maxFragmentLength > 0 and tLen > self.maxFragmentLength:
continue
# get rid of duplicate reads that have same position on each of the
# pairs
if self.ignoreDuplicates:
# Assuming more or less concordant reads, use the fragment bounds, otherwise the start positions
if tLen >= 0:
s = read.pos
e = s + tLen
else:
s = read.pnext
e = s - tLen
if read.reference_id != read.next_reference_id:
e = read.pnext
if lpos is not None and lpos == read.reference_start \
and (s, e, read.next_reference_id, read.is_reverse) in prev_pos:
continue
if lpos != read.reference_start:
prev_pos.clear()
lpos = read.reference_start
prev_pos.add((s, e, read.next_reference_id, read.is_reverse))
# since reads can be split (e.g. RNA-seq reads) each part of the
# read that maps is called a position block.
try:
position_blocks = fragmentFromRead_func(read)
except TypeError:
# the get_fragment_from_read functions returns None in some cases.
# Those cases are to be skipped, hence the continue line.
continue
last_eIdx = None
for fragmentStart, fragmentEnd in position_blocks:
if fragmentEnd is None or fragmentStart is None:
continue
fragmentLength = fragmentEnd - fragmentStart
if fragmentLength == 0:
continue
# skip reads that are not in the region being
# evaluated.
if fragmentEnd <= reg[0] or fragmentStart >= reg[1]:
continue
if fragmentStart < reg[0]:
fragmentStart = reg[0]
if fragmentEnd > reg[0] + len(coverages) * tileSize:
fragmentEnd = reg[0] + len(coverages) * tileSize
sIdx = vector_start + max((fragmentStart - reg[0]) // tileSize, 0)
eIdx = vector_start + min(np.ceil(float(fragmentEnd - reg[0]) / tileSize).astype('int'), nRegBins)
if eIdx >= len(coverages):
eIdx = len(coverages) - 1
if last_eIdx is not None:
sIdx = max(last_eIdx, sIdx)
if sIdx >= eIdx:
continue
# First bin
if fragmentEnd < reg[0] + (sIdx + 1) * tileSize:
_ = fragmentEnd - fragmentStart
else:
_ = reg[0] + (sIdx + 1) * tileSize - fragmentStart
if _ > tileSize:
_ = tileSize
coverages[sIdx] += _
_ = sIdx + 1
while _ < eIdx:
coverages[_] += tileSize
_ += 1
while eIdx - sIdx >= nRegBins:
eIdx -= 1
if eIdx > sIdx:
_ = fragmentEnd - (reg[0] + eIdx * tileSize)
if _ > tileSize:
_ = tileSize
elif _ < 0:
_ = 0
coverages[eIdx] += _
last_eIdx = eIdx
c += 1
if self.verbose:
endTime = time.time()
print("%s, processing %s (%.1f per sec) reads @ %s:%s-%s" % (
multiprocessing.current_process().name, c, c / (endTime - start_time), chrom, reg[0], reg[1]))
vector_start += nRegBins
# change zeros to NAN
if self.zerosToNans:
coverages[coverages == 0] = np.nan
return coverages
class Tester(object):
def __init__(self):
"""
The distribution of reads between the two bam files is as follows.
They cover 200 bp
0 100 200
|------------------------------------------------------------|
A ===============
===============
B =============== ===============
===============
===============
"""
import os
self.root = os.path.dirname(os.path.abspath(__file__)) + "/test/test_data/"
self.bamFile1 = self.root + "testA.bam"
self.bamFile2 = self.root + "testB.bam"
self.bamFile_PE = self.root + "test_paired2.bam"
self.chrom = '3R'
|
