def __init__(self, bamfile, desc = None, step = 1e6, out = sys.stderr): self._bam = None self._out = out self._desc = desc self._step = step self._count = 0 self._last_count = 0 self._last_time = time.time() self._start_time = self._last_time self._last_fract = -1.0 self._total = 0.0 self._counts = [] if bamfile and bamfile.header.get("HD", {}).get("SO", "NA") == "coordinate": self._bam = bamfile self._total = float(sum(bamfile.lengths)) or 1.0 self._counts.append(0) self._counts.extend(cumsum(bamfile.lengths))
def __init__(self, bamfile, desc=None, step=1e6, out=sys.stderr): self._bam = None self._out = out self._desc = desc self._step = step self._count = 0 self._last_count = 0 self._last_time = time.time() self._start_time = self._last_time self._last_fract = -1.0 self._total = 0.0 self._counts = [] if bamfile and bamfile.header.get("HD", {}).get("SO", "NA") == "coordinate": self._bam = bamfile self._total = float(sum(bamfile.lengths)) or 1.0 self._counts.append(0) self._counts.extend(cumsum(bamfile.lengths))
def test_cumsum__initial(): assert_equal(list(utils.cumsum(range(5), -10)), [-10, -9, -7, -4, 0])
def test_cumsum__float(): assert_equal(list(utils.cumsum((1.0, 2.0, 3.0))), [1.0, 3.0, 6.0])
def test_cumsum__integers(): assert_equal(list(utils.cumsum(range(-4, 5))), [-4, -7, -9, -10, -10, -9, -7, -4, 0])
def test_cumsum__empty(): assert_equal(list(utils.cumsum([])), [])