def _runTest(self, starts=None, ends=None, values=None, strands=None,
ids=None, edges=None, weights=None, newId=None,
expStarts=None, expEnds=None, expValues=None,
expStrands=None, expIds=None, expEdges=None,
expWeights=None, expExtras=None, customChrLength=None,
allowOverlap=True, resultAllowOverlap=False,
expTrackFormatType=None, debug=False):
track = createSimpleTestTrackContent(startList=starts, endList=ends,
valList=values,
strandList=strands,
idList=ids, edgeList=edges,
weightsList=weights,
customChrLength=customChrLength)
r = RemoveDeadLinks(track, newId=newId,
resultAllowOverlap=resultAllowOverlap,
debug=debug)
result = r.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:
# As weights can contain numpy.nan, we can not use the
# normal array_equal method.
# (np.nan == np.nan) == False
# Using the assert_equal instead which.
self.assertTrue(newWeights is not None)
try:
np.testing.assert_equal(newWeights, expWeights)
except AssertionError:
self.fail("Weights are not equal")
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)
def _runMultipleTest(self, t1Starts, t1Ends, t1Ids, t1Edges, t2Starts,
t2Ends, t2Ids, t2Edges, t1ExpStarts, t1ExpEnds,
t1ExpIds, t1ExpEdges, t2ExpStarts, t2ExpEnds,
t2ExpIds, t2ExpEdges, debug=False,
expTrackFormatType=None):
"""
Run test on multiple chromosomes.
:return:
"""
chr2 = (GenomeRegion('hg19', 'chr2', 0,
GenomeInfo.GENOMES['hg19']['size']['chr2']))
hg19 = Genome('hg19', GenomeInfo.GENOMES['hg19'])
t1Starts = np.array(t1Starts)
t1Ends = np.array(t1Ends)
t1Ids = np.array(t1Ids)
t1Edges = np.array(t1Edges)
t2Starts = np.array(t2Starts)
t2Ends = np.array(t2Ends)
t2Ids = np.array(t2Ids)
t2Edges = np.array(t2Edges)
tv1 = TrackView(self.chr1, t1Starts, t1Ends, None, None, t1Ids,
t1Edges, None, borderHandling='crop',
allowOverlaps=False, extraLists=OrderedDict())
tv2 = TrackView(chr2, t2Starts, t2Ends, None, None, t2Ids, t2Edges,
None, borderHandling='crop', allowOverlaps=False,
extraLists=OrderedDict())
tvs = OrderedDict()
tvs[self.chr1] = tv1
tvs[chr2] = tv2
track = TrackContents(hg19, tvs)
r = RemoveDeadLinks(track, useGlobal=True)
result = r.calculate()
self.assertTrue(result is not None)
chr1Found = False
chr2Found = False
for (k, v) in result.trackViews.iteritems():
starts = v.startsAsNumpyArray()
ends = v.endsAsNumpyArray()
ids = v.idsAsNumpyArray()
edges = v.edgesAsNumpyArray()
if cmp(k, self.chr1) == 0:
if debug:
print("newStarts: {}".format(starts))
print("t1ExpStarts: {}".format(t1ExpStarts))
print("newEnds: {}".format(ends))
print("t1ExpEnds: {}".format(t1ExpEnds))
print("newIds: {}".format(ids))
print("t1ExpIds: {}".format(t1ExpIds))
print("newEdges: {}".format(edges))
print("t1ExpEdges: {}".format(t1ExpEdges))
if expTrackFormatType is not None:
self.assertTrue(v.trackFormat.getFormatName() ==
expTrackFormatType)
self.assertTrue(np.array_equal(starts, t1ExpStarts))
self.assertTrue(np.array_equal(ends, t1ExpEnds))
self.assertTrue(np.array_equal(ids, t1ExpIds))
self.assertTrue(np.array_equal(edges, t1ExpEdges))
chr1Found = True
elif cmp(k, chr2) == 0:
if debug:
print("newStarts: {}".format(starts))
print("t2ExpStarts: {}".format(t2ExpStarts))
print("newEnds: {}".format(ends))
print("t2ExpEnds: {}".format(t2ExpEnds))
print("newIds: {}".format(ids))
print("t2ExpIds: {}".format(t2ExpIds))
print("newEdges: {}".format(edges))
print("t2ExpEdges: {}".format(t2ExpEdges))
if expTrackFormatType is not None:
self.assertTrue(v.trackFormat.getFormatName() ==
expTrackFormatType)
self.assertTrue(np.array_equal(starts, t2ExpStarts))
self.assertTrue(np.array_equal(ends, t2ExpEnds))
self.assertTrue(np.array_equal(ids, t2ExpIds))
self.assertTrue(np.array_equal(edges, t2ExpEdges))
chr2Found = True
else:
# Tests if all tracks no in chr1 have a size of 0.
self.assertEqual(v.size, 0)
self.assertTrue(chr1Found)
self.assertTrue(chr2Found)
