def _runWithProfiling(self, runStr, globals, locals):
if self.USE_PROFILER:
print 'Running with profiling..'
profiler = Profiler()
res = profiler.run(runStr, globals, locals)
profiler.printStats(graphDir=get_data_output_path(), id=self.__class__.__name__)
return res
else:
return eval(runStr, globals, locals)
def test_bedgraph(self):
bedgraph_fn = os.path.join(get_data_path(), "chrY_coverage.bedgraph")
trackfn = os.path.join(get_data_output_path(), "test_io_track")
track = load_bedgraph(bedgraph_fn, trackfn=trackfn)
self.assertEquals(len(track), 60)
first = tuple(track[0])
self.assertEquals(first, (24, 0L, 1000000L))
last = tuple(track[-1])
self.assertEquals(last, (24, 59000000, 59373566))
self.assertRaises(KeyError, track.get_node_values, "datax")
data = track.get_node_values("data")
self.assertEquals(len(data), 60)
self.assertTrue(data.shape == (60,))
track.close()
def get_fn(self):
#fd, fn = tempfile.mkstemp()
#os.close(fd)
trackfn = os.path.join(get_data_output_path(), 'test_core_track')
return trackfn
def get_fn(self):
#fd, fn = tempfile.mkstemp()
#os.close(fd)
trackfn = os.path.join(get_data_output_path(), 'test_core_track')
return trackfn