class NFRChunk(Chunk):
"""Class for storing and determining collection of nfr positions
"""
def __init__(self, chunk):
self.start = chunk.start
self.end = chunk.end
self.chrom = chunk.chrom
self.nfrs = []
def initialize(self, parameters):
self.params = parameters
def getOcc(self):
"""gets occupancy track-- reads in from bedgraph"""
self.occ = Track(self.chrom, self.start, self.end, "Occupancy")
self.occ.read_track(self.params.occ_track)
#lower_file = self.params.occ_track[:-11] + 'lower_bound.bedgraph.gz'
#self.occ_lower = Track(self.chrom,self.start,self.end,"Occupancy")
#self.occ_lower.read_track(lower_file)
upper_file = self.params.occ_track[:-11] + 'upper_bound.bedgraph.gz'
self.occ_upper = Track(self.chrom, self.start, self.end, "Occupancy")
self.occ_upper.read_track(upper_file)
def getIns(self):
"""gets insertion track-- reads in from bedgraph"""
if self.params.ins_track is None:
self.ins = InsertionTrack(self.chrom, self.start, self.end)
self.ins.calculateInsertions(self.params.bam)
else:
self.ins = Track(self.chrom, self.start, self.end, "Insertion")
self.ins.read_track(self.params.ins_track)
def getBias(self):
"""get bias"""
self.bias = InsertionBiasTrack(self.chrom,
self.start,
self.end,
log=True)
if self.params.fasta is not None:
self.bias.computeBias(self.params.fasta, self.params.chrs,
self.params.pwm)
def findNFRs(self):
"""find NFR regions"""
region = np.ones(self.length())
tbx = pysam.TabixFile(self.params.calls)
nucs = []
if self.chrom in tbx.contigs:
for row in tbx.fetch(self.chrom,
self.start,
self.end,
parser=pysam.asTuple()):
nucs.append(int(row[1]))
for j in xrange(1, len(nucs)):
left = nucs[j - 1] + 73
right = nucs[j] - 72
if right <= left:
continue
candidate = NFR(left, right, self)
if candidate.min_upper < self.params.max_occ_upper and candidate.occ < self.params.max_occ:
self.nfrs.append(candidate)
def process(self, params):
"""wrapper to carry out all methods needed to call nucleosomes and nfrs"""
self.initialize(params)
self.getOcc()
self.getIns()
self.getBias()
self.findNFRs()
def removeData(self):
"""remove data from chunk-- deletes all attributes"""
names = self.__dict__.keys()
for name in names:
delattr(self, name)
