Example #1
0
def _insHelper(arg):
    (chunk, args) = arg
    try:
        ins = InsertionTrack(chunk.chrom, chunk.start, chunk.end)
        ins.calculateInsertions( args.bam, lower = args.lower, upper = args.upper, atac = args.atac)
    except Exception as e:
        print('Caught exception when processing:\n'+  chunk.asBed()+"\n")
        traceback.print_exc()
        print()
        raise e
    return ins
Example #2
0
 def test_ins_methods(self):
     """test that two methods for getting insertion track give same result"""
     ins1 = InsertionTrack(self.chunk.chrom, self.chunk.start, self.chunk.end)
     ins1.calculateInsertions("example/single_read.bam")
     mat = FragmentMat2D(self.chunk.chrom, self.chunk.start, self.chunk.end, 0, 100)
     mat.makeFragmentMat("example/single_read.bam")
     ins2 = mat.getIns()
     self.assertTrue(
         np.array_equal(
             ins1.get(self.chunk.start + 100, self.chunk.start + 300),
             ins2.get(self.chunk.start + 100, self.chunk.start + 300),
         )
     )
Example #3
0
 def test_ins_methods(self):
     """test that two methods for getting insertion track give same result"""
     ins1 = InsertionTrack(self.chunk.chrom, self.chunk.start,
                           self.chunk.end)
     ins1.calculateInsertions('example/single_read.bam')
     mat = FragmentMat2D(self.chunk.chrom, self.chunk.start, self.chunk.end,
                         0, 100)
     mat.makeFragmentMat('example/single_read.bam')
     ins2 = mat.getIns()
     self.assertTrue(
         np.array_equal(
             ins1.get(self.chunk.start + 100, self.chunk.start + 300),
             ins2.get(self.chunk.start + 100, self.chunk.start + 300)))
Example #4
0
def _insHelperSmooth(arg):
    """Computes smoothed insertion track for a particular set of bed regions"""
    (chunk, args) = arg
    try:
        offset = args.smooth / 2
        ins = InsertionTrack(chunk.chrom, chunk.start - offset, chunk.end + offset)
        ins.calculateInsertions( args.bam, lower = args.lower, upper = args.upper, atac = args.atac)
        ins.smooth_track(args.smooth, window = "gaussian", mode= 'valid')
    except Exception as e:
        print('Caught exception when processing:\n'+  chunk.asBed()+"\n")
        traceback.print_exc()
        print()
        raise e
    return ins
Example #5
0
def _insHelper(arg):
    (chunk, args) = arg
    try:
        ins = InsertionTrack(chunk.chrom, chunk.start, chunk.end)
        ins.calculateInsertions(args.bam,
                                lower=args.lower,
                                upper=args.upper,
                                atac=args.atac)
    except Exception as e:
        print('Caught exception when processing:\n' + chunk.asBed() + "\n")
        traceback.print_exc()
        print()
        raise e
    return ins
Example #6
0
 def getIns(self):
     """Collape matrix into insertions.  Will reduce span on chromosome"""
     pattern = np.zeros(
         (self.upper - self.lower, self.upper + (self.upper - 1) % 2))
     mid = self.upper / 2
     for i in range(self.lower, self.upper):
         pattern[i - self.lower, mid + (i - 1) / 2] = 1
         pattern[i - self.lower, mid - (i / 2)] = 1
     ins = signal.correlate2d(self.mat, pattern, mode="valid")[0]
     insertion_track = InsertionTrack(self.chrom,
                                      self.start + pattern.shape[1] / 2,
                                      self.end - (pattern.shape[1] / 2))
     insertion_track.assign_track(ins)
     return insertion_track
Example #7
0
def _pwmHelper(arg):
    """"Helper function for multiprocessing acquisition of sequence around insertions"""
    (chunks, params) = arg
    try:
        n = 0.0
        mat = np.zeros((len(params.nucleotides), params.up + params.down + 1))
        for chunk in chunks:
            ins = InsertionTrack(chunk.chrom, chunk.start, chunk.end)
            if params.sym:
                ins.calculateInsertions(params.bam,
                                        lower=params.lower,
                                        upper=params.upper,
                                        atac=params.atac)
                mat += ins.getInsertionSequences(params.fasta,
                                                 params.nucleotides,
                                                 up=params.up,
                                                 down=params.down)
            else:
                ins.calculateStrandedInsertions(params.bam,
                                                lower=params.lower,
                                                upper=params.upper,
                                                atac=params.atac)
                mat += ins.getStrandedInsertionSequences(params.fasta,
                                                         params.nucleotides,
                                                         up=params.up,
                                                         down=params.down)
            n += sum(ins.vals)
    except Exception as e:
        print('Caught exception when processing:\n' + chunk.asBed() + "\n")
        traceback.print_exc()
        print()
        raise e
    return mat, n
Example #8
0
 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)
Example #9
0
def _pwmHelper(arg):
    """"Helper function for multiprocessing acquisition of sequence around insertions"""
    (chunks, params) = arg
    try:
        n = 0.0
        mat = np.zeros((len(params.nucleotides), params.up + params.down + 1))
        for chunk in chunks:
            ins = InsertionTrack(chunk.chrom, chunk.start, chunk.end)
            if params.sym:
                ins.calculateInsertions( params.bam, lower = params.lower, upper = params.upper, atac = params.atac)
                mat += ins.getInsertionSequences(params.fasta, params.nucleotides, up = params.up, down = params.down)
            else:
                ins.calculateStrandedInsertions( params.bam, lower = params.lower, upper = params.upper, atac = params.atac)
                mat += ins.getStrandedInsertionSequences(params.fasta, params.nucleotides, up = params.up, down = params.down)
            n += sum(ins.vals)
    except Exception as e:
        print('Caught exception when processing:\n'+  chunk.asBed()+"\n")
        traceback.print_exc()
        print()
        raise e
    return mat, n
Example #10
0
def _insHelperSmooth(arg):
    """Computes smoothed insertion track for a particular set of bed regions"""
    (chunk, args) = arg
    try:
        offset = args.smooth / 2
        ins = InsertionTrack(chunk.chrom, chunk.start - offset,
                             chunk.end + offset)
        ins.calculateInsertions(args.bam,
                                lower=args.lower,
                                upper=args.upper,
                                atac=args.atac)
        ins.smooth_track(args.smooth, window="gaussian", mode='valid')
    except Exception as e:
        print('Caught exception when processing:\n' + chunk.asBed() + "\n")
        traceback.print_exc()
        print()
        raise e
    return ins