def _create_h5obj(self):
if self.name in self._parent:
self.group = self._parent[self.name]
else:
gcpl = h5py.h5p.create(h5py.h5p.GROUP_CREATE)
flags = h5py.h5p.CRT_ORDER_TRACKED | h5py.h5p.CRT_ORDER_INDEXED
gcpl.set_link_creation_order(flags)
name = self.name.encode("utf-8")
gid = h5py.h5g.create(self._parent.id, name, gcpl=gcpl)
self.group = h5py.Group(gid)
def create_h5group(parent, name):
"""
Creates an h5group with the given name under the given parent using the
same flags and properties used in NIX (creation order tracking and
indexing).
"""
gcpl = h5py.h5p.create(h5py.h5p.GROUP_CREATE)
flags = h5py.h5p.CRT_ORDER_TRACKED | h5py.h5p.CRT_ORDER_INDEXED
gcpl.set_link_creation_order(flags)
name = name.encode("utf-8")
gid = h5py.h5g.create(parent.id, name, gcpl=gcpl)
return h5py.Group(gid)
def main():
logger.debug("%s starting" % sys.argv[0])
opt, args = getParms()
infile_name = args[0]
infile = h5py.File(infile_name, 'r')
colours = ('grey', 'red', 'green')
legends = ('non-seq', 'prod-0', 'prod-1')
top = h5py.Group(infile, '/')
ZMW = top["PulseData/BaseCalls/ZMW"]
ZMWMetrics = top["PulseData/BaseCalls/ZMWMetrics"]
holeStatus = ZMW["HoleStatus"]
holeXY = ZMW["HoleXY"]
holeProd = ZMWMetrics["Productivity"]
nonseqHoles = holeStatus[:] != 0 # ZMWs other than sequencing
prod0Holes = np.logical_and(holeProd[:] == 0, np.logical_not(nonseqHoles))
prod1Holes = np.logical_and(holeProd[:] == 1, np.logical_not(nonseqHoles))
holesByType = (nonseqHoles, prod0Holes, prod1Holes)
for which in xrange(len(holesByType)):
whichHoles = holesByType[which]
howMany = sum(whichHoles)
logger.debug("%5d %s" % (howMany, legends[which]))
if howMany > 0:
plt.scatter (holeXY[whichHoles,0], holeXY[whichHoles,1], \
s=1, c=colours[which], edgecolor='face', \
label="%5d %s" % (howMany, legends[which]))
plt.axis('equal')
plt.legend(scatterpoints=3, prop={'size': 8})
plt.savefig(opt.output)
infile.close()
logger.debug("complete")
def main():
logger.debug("%s starting" % sys.argv[0])
opt, args = getParms()
infile_name = args[0]
infile = h5py.File(infile_name, 'r')
colours = ('#aaaaaa', '#ff0000', '#00ff00', '#0000ff', '#ff0080',
'#8000ff', '#80ff00', '#ff8000', '#ffff00')
holeStatusTable = ('SEQUENCING', 'ANTIHOLE', 'FIDUCIAL', 'SUSPECT', \
'ANTIMIRROR', 'FDZMW', 'FBZMW', 'ANTIBEAMLET', 'OUTSIDEFOV')
top = h5py.Group(infile, '/')
ZMW = top["PulseData/BaseCalls/ZMW"]
holeStatus = ZMW["HoleStatus"]
holeXY = ZMW["HoleXY"]
for num in xrange(len(holeStatusTable)):
whichHoles = holeStatus[:] == num
HowMany = sum(whichHoles)
logger.debug("%5d ZMWs %d %s" % (HowMany, num, holeStatusTable[num]))
if HowMany > 0:
plt.scatter (holeXY[whichHoles,0], holeXY[whichHoles,1], \
s=1, c=colours[num], edgecolor='face', \
label="%d %5d %s" % (num, HowMany, holeStatusTable[num]))
plt.axis('equal')
plt.legend(scatterpoints=3, prop={'size': 8})
plt.savefig(opt.output)
infile.close()
logger.debug("complete")