def test_len(self): # AlignmentSet aln = AlignmentSet(data.getXml(8), strict=True) self.assertEqual(len(aln), 92) self.assertEqual(aln._length, (92, 123588)) self.assertEqual(aln.totalLength, 123588) self.assertEqual(aln.numRecords, 92) aln.totalLength = -1 aln.numRecords = -1 self.assertEqual(aln.totalLength, -1) self.assertEqual(aln.numRecords, -1) aln.updateCounts() self.assertEqual(aln.totalLength, 123588) self.assertEqual(aln.numRecords, 92) self.assertEqual(sum(1 for _ in aln), 92) self.assertEqual(sum(len(rec) for rec in aln), 123588) # AlignmentSet with filters aln = AlignmentSet(data.getXml(15), strict=True) self.assertEqual(len(aln), 40) self.assertEqual(aln._length, (40, 52023)) self.assertEqual(aln.totalLength, 52023) self.assertEqual(aln.numRecords, 40) aln.totalLength = -1 aln.numRecords = -1 self.assertEqual(aln.totalLength, -1) self.assertEqual(aln.numRecords, -1) aln.updateCounts() self.assertEqual(aln.totalLength, 52023) self.assertEqual(aln.numRecords, 40) # SubreadSet sset = SubreadSet(data.getXml(10), strict=True) self.assertEqual(len(sset), 92) self.assertEqual(sset._length, (92, 124093)) self.assertEqual(sset.totalLength, 124093) self.assertEqual(sset.numRecords, 92) sset.totalLength = -1 sset.numRecords = -1 self.assertEqual(sset.totalLength, -1) self.assertEqual(sset.numRecords, -1) sset.updateCounts() self.assertEqual(sset.totalLength, 124093) self.assertEqual(sset.numRecords, 92) self.assertEqual(sum(1 for _ in sset), 92) self.assertEqual(sum(len(rec) for rec in sset), 124093) # ReferenceSet sset = ReferenceSet(data.getXml(9), strict=True) self.assertEqual(len(sset), 59) self.assertEqual(sset.totalLength, 85774) self.assertEqual(sset.numRecords, 59) sset.totalLength = -1 sset.numRecords = -1 self.assertEqual(sset.totalLength, -1) self.assertEqual(sset.numRecords, -1) sset.updateCounts() self.assertEqual(sset.totalLength, 85774) self.assertEqual(sset.numRecords, 59)
def test_len(self): # AlignmentSet aln = AlignmentSet(data.getXml(7), strict=True) assert len(aln) == 92 assert aln._length == (92, 123588) assert aln.totalLength == 123588 assert aln.numRecords == 92 aln.totalLength = -1 aln.numRecords = -1 assert aln.totalLength == -1 assert aln.numRecords == -1 aln.updateCounts() assert aln.totalLength == 123588 assert aln.numRecords == 92 assert sum(1 for _ in aln) == 92 assert sum(len(rec) for rec in aln) == 123588 # AlignmentSet with filters aln = AlignmentSet(data.getXml(14), strict=True) assert len(aln) == 40 assert aln._length == (40, 52023) assert aln.totalLength == 52023 assert aln.numRecords == 40 aln.totalLength = -1 aln.numRecords = -1 assert aln.totalLength == -1 assert aln.numRecords == -1 aln.updateCounts() assert aln.totalLength == 52023 assert aln.numRecords == 40 # SubreadSet sset = SubreadSet(data.getXml(9), strict=True) assert len(sset) == 92 assert sset._length == (92, 124093) assert sset.totalLength == 124093 assert sset.numRecords == 92 sset.totalLength = -1 sset.numRecords = -1 assert sset.totalLength == -1 assert sset.numRecords == -1 sset.updateCounts() assert sset.totalLength == 124093 assert sset.numRecords == 92 assert sum(1 for _ in sset) == 92 assert sum(len(rec) for rec in sset) == 124093 # ReferenceSet sset = ReferenceSet(data.getXml(8), strict=True) assert len(sset) == 59 assert sset.totalLength == 85774 assert sset.numRecords == 59 sset.totalLength = -1 sset.numRecords = -1 assert sset.totalLength == -1 assert sset.numRecords == -1 sset.updateCounts() assert sset.totalLength == 85774 assert sset.numRecords == 59
def test_len(self): # AlignmentSet aln = AlignmentSet(data.getXml(8), strict=True) self.assertEqual(len(aln), 92) self.assertEqual(aln._length, (92, 123588)) self.assertEqual(aln.totalLength, 123588) self.assertEqual(aln.numRecords, 92) aln.totalLength = -1 aln.numRecords = -1 self.assertEqual(aln.totalLength, -1) self.assertEqual(aln.numRecords, -1) aln.updateCounts() self.assertEqual(aln.totalLength, 123588) self.assertEqual(aln.numRecords, 92) self.assertEqual(sum(1 for _ in aln), 92) self.assertEqual(sum(len(rec) for rec in aln), 123588) # AlignmentSet with filters aln = AlignmentSet(data.getXml(15), strict=True) self.assertEqual(len(aln), 40) self.assertEqual(aln._length, (40, 52023)) self.assertEqual(aln.totalLength, 52023) self.assertEqual(aln.numRecords, 40) aln.totalLength = -1 aln.numRecords = -1 self.assertEqual(aln.totalLength, -1) self.assertEqual(aln.numRecords, -1) aln.updateCounts() self.assertEqual(aln.totalLength, 52023) self.assertEqual(aln.numRecords, 40) # AlignmentSet with cmp.h5 aln = AlignmentSet(upstreamData.getBamAndCmpH5()[1], strict=True) self.assertEqual(len(aln), 112) self.assertEqual(aln._length, (112, 59970)) self.assertEqual(aln.totalLength, 59970) self.assertEqual(aln.numRecords, 112) aln.totalLength = -1 aln.numRecords = -1 self.assertEqual(aln.totalLength, -1) self.assertEqual(aln.numRecords, -1) aln.updateCounts() self.assertEqual(aln.totalLength, 59970) self.assertEqual(aln.numRecords, 112) # SubreadSet sset = SubreadSet(data.getXml(10), strict=True) self.assertEqual(len(sset), 92) self.assertEqual(sset._length, (92, 124093)) self.assertEqual(sset.totalLength, 124093) self.assertEqual(sset.numRecords, 92) sset.totalLength = -1 sset.numRecords = -1 self.assertEqual(sset.totalLength, -1) self.assertEqual(sset.numRecords, -1) sset.updateCounts() self.assertEqual(sset.totalLength, 124093) self.assertEqual(sset.numRecords, 92) self.assertEqual(sum(1 for _ in sset), 92) self.assertEqual(sum(len(rec) for rec in sset), 124093) # HdfSubreadSet # len means something else in bax/bas land. These numbers may actually # be correct... sset = HdfSubreadSet(data.getXml(17), strict=True) self.assertEqual(len(sset), 9) self.assertEqual(sset._length, (9, 128093)) self.assertEqual(sset.totalLength, 128093) self.assertEqual(sset.numRecords, 9) sset.totalLength = -1 sset.numRecords = -1 self.assertEqual(sset.totalLength, -1) self.assertEqual(sset.numRecords, -1) sset.updateCounts() self.assertEqual(sset.totalLength, 128093) self.assertEqual(sset.numRecords, 9) # ReferenceSet sset = ReferenceSet(data.getXml(9), strict=True) self.assertEqual(len(sset), 59) self.assertEqual(sset.totalLength, 85774) self.assertEqual(sset.numRecords, 59) sset.totalLength = -1 sset.numRecords = -1 self.assertEqual(sset.totalLength, -1) self.assertEqual(sset.numRecords, -1) sset.updateCounts() self.assertEqual(sset.totalLength, 85774) self.assertEqual(sset.numRecords, 59)