def _preCalculation(self):
t1 = self._tracks[0]
t2 = self._tracks[1]
print("**************")
print(t1.trackFormat)
print(t2.trackFormat)
print("**************")
if t1.trackFormat.isLinked():
u = UniquifyLinks(t1, identifier="track-1")
t1 = u.calculate()
if t2.trackFormat.isLinked():
u = UniquifyLinks(t2, identifier="track-2")
t2 = u.calculate()
self._tracks = [t1, t2]
def _runTest(self, ids, edges, expIds, expEdges, starts=None,
ends=None, values=None, strands=None, weights=None,
expStarts=None, expEnds=None, expValues=None, expStrands=None,
expWeights=None, expExtras=None, expTrackFormatType=None,
trackIdentifier=None, customChrLength=None, debug=False):
track = createSimpleTestTrackContent(startList=starts, endList=ends,
valList=values,
strandList=strands,
idList=ids, edgeList=edges,
weightsList=weights,
customChrLength=customChrLength)
u = UniquifyLinks(track, identifier=trackIdentifier, debug=debug)
result = u.calculate()
self.assertTrue(result is not None)
resFound = False
for (k, v) in result.getTrackViews().iteritems():
if cmp(k, self.chr1) == 0 or cmp(k, self.chr1Small) == 0:
# All test tracks are in chr1
resFound = True
newStarts = v.startsAsNumpyArray()
newEnds = v.endsAsNumpyArray()
newValues = v.valsAsNumpyArray()
newStrands = v.strandsAsNumpyArray()
newIds = v.idsAsNumpyArray()
newEdges = v.edgesAsNumpyArray()
newWeights = v.weightsAsNumpyArray()
newExtras = v.allExtrasAsDictOfNumpyArrays()
if debug:
print("newTrackFormatType: {}".format(v.trackFormat))
print("expTrackFormatType: {}".format(expTrackFormatType))
print("newStarts: {}".format(newStarts))
print("expStarts: {}".format(expStarts))
print("newEnds: {}".format(newEnds))
print("expEnds: {}".format(expEnds))
print("newStrands: {}".format(newStrands))
print("expStrands: {}".format(expStrands))
print("newIds: {}".format(newIds))
print("expIds: {}".format(expIds))
print("newEdges: {}".format(newEdges))
print("expEdges: {}".format(expEdges))
print("newWeights: {}".format(newWeights))
print("expWeights: {}".format(expWeights))
if expTrackFormatType is not None:
self.assertTrue(v.trackFormat.getFormatName() ==
expTrackFormatType)
if expEnds is None and expStarts is not None:
# Assuming a point type track. Creating the expected ends.
expEnds = np.array(expStarts) + 1
if expStarts is not None:
self.assertTrue(newStarts is not None)
self.assertTrue(np.array_equal(newStarts, expStarts))
else:
self.assertTrue(newStarts is None)
if expEnds is not None:
self.assertTrue(newEnds is not None)
self.assertTrue(np.array_equal(newEnds, expEnds))
else:
self.assertTrue(newEnds is None)
if expValues is not None:
self.assertTrue(newValues is not None)
self.assertTrue(np.array_equal(newValues, expValues))
else:
self.assertTrue(newValues is None)
if expStrands is not None:
self.assertTrue(newStrands is not None)
self.assertTrue(np.array_equal(newStrands, expStrands))
else:
self.assertTrue(newStrands is None)
if expIds is not None:
self.assertTrue(newIds is not None)
self.assertTrue(np.array_equal(newIds, expIds))
else:
self.assertTrue(newIds is None)
if expEdges is not None:
self.assertTrue(newEdges is not None)
self.assertTrue(np.array_equal(newEdges, expEdges))
else:
self.assertTrue(newEdges is None)
if expWeights is not None:
self.assertTrue(newWeights is not None)
self.assertTrue(np.array_equal(newWeights, expWeights))
else:
self.assertTrue(newWeights is None)
if expExtras is not None:
for key in expExtras.keys():
self.assertTrue(v.hasExtra(key))
expExtra = expExtras[key]
newExtra = newExtras[key]
self.assertTrue(np.array_equal(newExtra, expExtra))
else:
self.assertTrue(len(newExtras) == 0)
else:
# Tests if all tracks no in chr1 have a size of 0.
self.assertEqual(v.size, 0)
self.assertTrue(resFound)