def testLazyChemistryResolution(self): """ The CmpH5Reader allows reading of files that have missing chemistry information---an exception will be thrown only upon attempts to access the information. We need to retain this behavior for compatibility. """ oldCmpH5 = data.getCmpH5() C = CmpH5Reader(oldCmpH5) # no exception here with assert_raises(ChemistryLookupError): C.sequencingChemistry with assert_raises(ChemistryLookupError): C[0].sequencingChemistry
def test___init__(self): cmpH5_format = CS.CmpH5Format(h.File(data.getCmpH5(), "r")) assert_equal(cmpH5_format.ALN_INFO, 'AlnInfo')
def __init__(self): self.h5FileName = data.getCmpH5() self.cmpH5 = CmpH5Reader(self.h5FileName)
def test_openFromH5File(self): cmpH5Filename = data.getCmpH5() c = CmpH5Reader(h5py.File(cmpH5Filename, "r")) EQ("1.2.0.SF", c.version)
def __init__(self): cmpH5Filename = data.getCmpH5() self._inCmpH5 = CmpH5Reader(cmpH5Filename) self.hit0 = self._inCmpH5[0] self.hit1 = self._inCmpH5[1]
def test_get_cmp_h5(self): assert data.getCmpH5().endswith(".cmp.h5")
def setup_class(self): self.h5FileName = data.getCmpH5() self.cmpH5 = CmpH5Reader(self.h5FileName)
def test_alignmentset_index(self): aln = AlignmentSet(upstreamData.getCmpH5(), strict=True) reads = aln.readsInRange(aln.refNames[0], 0, 1000) self.assertEqual(len(list(reads)), 2) self.assertEqual(len(list(aln)), 84) self.assertEqual(len(aln.index), 84)
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) # 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.getCmpH5(), strict=True) self.assertEqual(len(aln), 84) self.assertEqual(aln._length, (84, 26103)) self.assertEqual(aln.totalLength, 26103) self.assertEqual(aln.numRecords, 84) aln.totalLength = -1 aln.numRecords = -1 self.assertEqual(aln.totalLength, -1) self.assertEqual(aln.numRecords, -1) aln.updateCounts() self.assertEqual(aln.totalLength, 26103) self.assertEqual(aln.numRecords, 84) # 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) # 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)
def test___init__(self): cmpH5_format = CS.CmpH5Format(h.File(data.getCmpH5(),"r")) assert_equal(cmpH5_format.ALN_INFO, 'AlnInfo')