def testExtra(self):
tf = TrackFormat.createInstanceFromPrefixList(["start", "a", "b", "c"], "float64", 1, "float64", 1)
self.assertTrue(tf.hasExtra(specificExtra="a"))
self.assertFalse(tf.hasExtra(specificExtra="d"))
self.assertEqual(["a", "b", "c"], tf.getExtraNames())
tfq = TrackFormatReq(interval=False, extra=["a", "b"])
self.assertFalse(tfq.isCompatibleWith(tf))
def _assertConvertSegmentToPoint(self, targetStarts, sourceTv, converterCls):
pointFormat = TrackFormatReq(interval=False, dense=False)
self.assertTrue(converterCls.canHandle(sourceTv.trackFormat, pointFormat))
targetTv = converterCls.convert(sourceTv)
self.assertTrue(pointFormat.isCompatibleWith(targetTv.trackFormat))
self.assertEqual(targetStarts, [el.start() for el in targetTv])
for el in targetTv:
self.assertEqual(el.start() + 1, el.end())
def testValTypes(self):
tf = TrackFormat.createInstanceFromPrefixList(["start", "val"], "float128", 2, "float64", 1)
self.assertTrue(tf.isValued(specificValType="mean_sd"))
self.assertFalse(tf.isValued(specificValType="number"))
self.assertEqual("Mean and std.dev.", tf.getValTypeName())
self.assertEqual("Valued points", tf.getFormatName())
tfq = TrackFormatReq(interval=False, val="tc")
self.assertFalse(tfq.isCompatibleWith(tf))
def testWeightTypes(self):
tf = TrackFormat.createInstanceFromPrefixList(["id", "edges", "weights"], "float64", 1, "S8", 3)
self.assertTrue(tf.isWeighted(specificWeightType="category_vector"))
self.assertFalse(tf.isWeighted(specificWeightType="number"))
self.assertEqual("Vector of categories", tf.getWeightTypeName())
self.assertEqual("Linked base pairs", tf.getFormatName())
tfq = TrackFormatReq(linked=True, weights="number")
self.assertFalse(tfq.isCompatibleWith(tf))
def testExtra(self):
tf = TrackFormat.createInstanceFromPrefixList(['start', 'a', 'b', 'c'],
'float64', 1, 'float64',
1)
self.assertTrue(tf.hasExtra(specificExtra='a'))
self.assertFalse(tf.hasExtra(specificExtra='d'))
self.assertEqual(['a', 'b', 'c'], tf.getExtraNames())
tfq = TrackFormatReq(interval=False, extra=['a', 'b'])
self.assertFalse(tfq.isCompatibleWith(tf))
def _assertConvertSegmentToPoint(self, targetStarts, sourceTv,
converterCls):
pointFormat = TrackFormatReq(interval=False, dense=False)
self.assertTrue(
converterCls.canHandle(sourceTv.trackFormat, pointFormat))
targetTv = converterCls.convert(sourceTv)
self.assertTrue(pointFormat.isCompatibleWith(targetTv.trackFormat))
self.assertEqual(targetStarts, [el.start() for el in targetTv])
for el in targetTv:
self.assertEqual(el.start() + 1, el.end())
def testWeightTypes(self):
tf = TrackFormat.createInstanceFromPrefixList(
['id', 'edges', 'weights'], 'float64', 1, 'S8', 3)
self.assertTrue(tf.isWeighted(specificWeightType='category_vector'))
self.assertFalse(tf.isWeighted(specificWeightType='number'))
self.assertEqual('Vector of categories', tf.getWeightTypeName())
self.assertEqual('Linked base pairs', tf.getFormatName())
tfq = TrackFormatReq(linked=True, weights='number')
self.assertFalse(tfq.isCompatibleWith(tf))
def testCompatibilityWithExceptions(self):
tf = TrackFormat.createInstanceFromPrefixList(['start', 'val'],
'float64', 1, 'float64',
1)
self.assertFalse(TrackFormatReq(interval=True, strand=True, val='number')\
.isCompatibleWith(tf))
self.assertFalse(TrackFormatReq(interval=True, strand=True, val='number')\
.isCompatibleWith(tf, ['interval']))
self.assertTrue(TrackFormatReq(interval=True, strand=True, val='number')\
.isCompatibleWith(tf, ['interval', 'hasStrand']))
self.assertFalse(TrackFormatReq(interval=True, strand=True, val='tc')\
.isCompatibleWith(tf, ['interval', 'hasStrand']))
def testValTypes(self):
tf = TrackFormat.createInstanceFromPrefixList(['start', 'val'],
'float128', 2, 'float64',
1)
self.assertTrue(tf.isValued(specificValType='mean_sd'))
self.assertFalse(tf.isValued(specificValType='number'))
self.assertEqual('Mean and std.dev.', tf.getValTypeName())
self.assertEqual('Valued points', tf.getFormatName())
tfq = TrackFormatReq(interval=False, val='tc')
self.assertFalse(tfq.isCompatibleWith(tf))
def testMerge(self):
mergedTFR = TrackFormatReq.merge(TrackFormatReq(dense=False), TrackFormatReq(interval=True))
self.assertFalse(mergedTFR.isDense())
self.assertTrue(mergedTFR.isInterval())
mergedTFR = TrackFormatReq.merge(
TrackFormatReq(dense=False, val="tc"), TrackFormatReq(interval=True, val="number")
)
self.assertEqual(None, mergedTFR)
mergedTFR = TrackFormatReq.merge(
TrackFormatReq(dense=False, weights="tc"), TrackFormatReq(interval=True, weights="number")
)
self.assertEqual(None, mergedTFR)
def addFormatReq(self, requestedTrackFormat):
prevFormatReq = self._trackFormatReq
self._trackFormatReq = TrackFormatReq.merge(self._trackFormatReq,
requestedTrackFormat)
if self._trackFormatReq is None:
raise IncompatibleTracksError(str(prevFormatReq ) + \
' is incompatible with additional ' + str(requestedTrackFormat))
def testMerge(self):
mergedTFR = TrackFormatReq.merge(TrackFormatReq(dense=False),
TrackFormatReq(interval=True))
self.assertFalse(mergedTFR.isDense())
self.assertTrue(mergedTFR.isInterval())
mergedTFR = TrackFormatReq.merge(
TrackFormatReq(dense=False, val='tc'),
TrackFormatReq(interval=True, val='number'))
self.assertEqual(None, mergedTFR)
mergedTFR = TrackFormatReq.merge(
TrackFormatReq(dense=False, weights='tc'),
TrackFormatReq(interval=True, weights='number'))
self.assertEqual(None, mergedTFR)
def _assertFunctions(self,
tf,
formatName,
dense,
valued,
interval,
linked,
reprDense,
strand,
id,
weighted,
hasExtra,
val='number',
weights='number',
extra=[]):
self.assertEqual(dense, tf.isDense())
self.assertEqual(valued, tf.isValued())
if valued:
self.assertEqual(TrackFormat.VAL_TYPE_NAME_DICT[val],
tf.getValTypeName())
self.assertEqual(interval, tf.isInterval())
self.assertEqual(linked, tf.isLinked())
if reprDense != None:
self.assertEqual(reprDense, tf.reprIsDense())
self.assertEqual(strand, tf.hasStrand())
self.assertEqual(id, tf.hasId())
self.assertEqual(weighted, tf.isWeighted())
if weighted:
self.assertEqual(TrackFormat.VAL_TYPE_NAME_DICT[weights],
tf.getWeightTypeName())
self.assertEqual(hasExtra, tf.hasExtra())
if extra:
self.assertEqual(extra, tf.getExtraNames())
if not str(tf).startswith('Requirement'):
self.assertEqual(formatName, tf.getFormatName())
#To test TrackFormatReq(name=formatName) on the standard formats in an easy way
self.assertTrue(
TrackFormatReq(name=formatName).isCompatibleWith(tf))
def testFormatsReqs(self):
for dense in (False, True, None):
for val in (False, 'number', 'category_vector', None):
for interval in (False, True, None):
for linked in (False, True, None):
for strand in (False, True, None):
for id in (False, True, None):
if linked == True and id == False:
continue
for weights in (False, 'tc', 'char_vector',
None):
if linked == False and weights not in [
False, None
]:
continue
for extra in (False, ['a', 'b'], None):
tfReq = TrackFormatReq(dense=dense, val=val, interval=interval, linked=linked, \
strand=strand, id=id, weights=weights, extra=extra)
self._assertFormatsReqs(
tfReq, dense, val, interval,
linked, strand, id, weights, extra)
def __init__(self, trackName, **kwArgs):
Track.__init__(self, trackName, **kwArgs)
self.addFormatReq(
TrackFormatReq(allowOverlaps=False, borderHandling='crop'))
def _isDenseTrack(self):
try:
return TrackFormatReq(name=self.trackFormatName).isDense()
except:
return False
def _getTrack(self):
track = Track(self._trackName)
track.addFormatReq(TrackFormatReq(allowOverlaps=self._allowOverlaps))
return track
def testConvertSegmentToPointReqFails(self):
segSourceTv = SampleTV(segments=[[2, 20], [7, 11]])
self._assertFailedConversion(segSourceTv, \
TrackFormatReq(interval=False, dense=False, val='category'))
self._assertFailedConversion(segSourceTv, \
TrackFormatReq(interval=False, dense=False, strand=True))
def _getTrackView(self, trackName, region, allowOverlaps):
track = Track(trackName)
track.addFormatReq(TrackFormatReq(allowOverlaps=allowOverlaps))
return track.getTrackView(region)
def addFormatReq(self, requestedTrackFormat):
prevFormatReq = self._trackFormatReq
self._trackFormatReq = TrackFormatReq.merge(self._trackFormatReq, requestedTrackFormat)
if self._trackFormatReq is None:
raise IncompatibleTracksError(str(prevFormatReq ) + \
' is incompatible with additional ' + str(requestedTrackFormat))