def getReadAlignmentId(self, gaAlignment):
"""
Returns a string ID suitable for use in the specified GA
ReadAlignment object in this ReadGroup.
"""
compoundId = datamodel.ReadAlignmentCompoundId(
self.getCompoundId(), gaAlignment.fragmentName)
return str(compoundId)
def assertAlignmentsEqual(self, gaAlignment, pysamAlignment,
readGroupInfo):
if pysamAlignment.query_qualities is None:
self.assertEqual(gaAlignment.alignedQuality, [])
else:
self.assertEqual(gaAlignment.alignedQuality,
list(pysamAlignment.query_qualities))
self.assertEqual(gaAlignment.alignedSequence,
pysamAlignment.query_sequence)
self.assertEqual(gaAlignment.alignment.mappingQuality,
pysamAlignment.mapping_quality)
self.assertEqual(
gaAlignment.alignment.position.referenceName,
readGroupInfo.samFile.getrname(pysamAlignment.reference_id))
self.assertEqual(gaAlignment.alignment.position.position,
pysamAlignment.reference_start)
# TODO test reverseStrand on position and on nextMatePosition once
# it has been implemented.
self.assertCigarEqual(gaAlignment.alignment.cigar,
pysamAlignment.cigar)
self.assertFlag(gaAlignment.duplicateFragment, pysamAlignment,
reads.SamFlags.DUPLICATE_FRAGMENT)
self.assertFlag(gaAlignment.failedVendorQualityChecks, pysamAlignment,
reads.SamFlags.FAILED_VENDOR_QUALITY_CHECKS)
self.assertEqual(gaAlignment.fragmentLength,
pysamAlignment.template_length)
self.assertEqual(gaAlignment.fragmentName, pysamAlignment.query_name)
compoundId = datamodel.ReadAlignmentCompoundId(
readGroupInfo.gaReadGroup.getCompoundId(),
pysamAlignment.query_name)
self.assertEqual(gaAlignment.id, str(compoundId))
self.assertEqual(
gaAlignment.info,
{key: [str(value)]
for key, value in pysamAlignment.tags})
if pysamAlignment.next_reference_id != -1:
self.assertEqual(gaAlignment.nextMatePosition.position,
pysamAlignment.next_reference_start)
self.assertEqual(
gaAlignment.nextMatePosition.referenceName,
readGroupInfo.samFile.getrname(
pysamAlignment.next_reference_id))
else:
self.assertIsNone(gaAlignment.nextMatePosition)
self.assertFlag(gaAlignment.properPlacement, pysamAlignment,
reads.SamFlags.PROPER_PLACEMENT)
self.assertEqual(gaAlignment.readGroupId, readGroupInfo.id)
self.assertFlag(gaAlignment.secondaryAlignment, pysamAlignment,
reads.SamFlags.SECONDARY_ALIGNMENT)
self.assertFlag(gaAlignment.supplementaryAlignment, pysamAlignment,
reads.SamFlags.SUPPLEMENTARY_ALIGNMENT)
def testReadAlignment(self):
readGroup = self.getReadGroup()
readGroupSet = readGroup.getParentContainer()
dataset = readGroupSet.getParentContainer()
localId = "alignment"
cid = datamodel.ReadAlignmentCompoundId(readGroupSet.getCompoundId(),
localId)
self.assertRaises(ValueError, datamodel.ReadAlignmentCompoundId,
dataset.getCompoundId())
self.assertEqual(cid.dataset, dataset.getLocalId())
self.assertEqual(cid.read_group_set, readGroupSet.getLocalId())
self.assertEqual(cid.read_alignment, localId)
self.assertEqual(cid.dataset_id, dataset.getId())
self.assertEqual(cid.read_group_set_id, readGroupSet.getId())
def assertAlignmentsEqual(self, gaAlignment, pysamAlignment,
readGroupInfo):
if pysamAlignment.query_qualities is None:
self.assertEqual(gaAlignment.alignedQuality, [])
else:
self.assertEqual(gaAlignment.alignedQuality,
list(pysamAlignment.query_qualities))
self.assertEqual(gaAlignment.alignedSequence,
pysamAlignment.query_sequence)
if reads.SamFlags.isFlagSet(pysamAlignment.flag,
reads.SamFlags.READ_UNMAPPED):
self.assertIsNone(gaAlignment.alignment)
else:
self.assertEqual(gaAlignment.alignment.mappingQuality,
pysamAlignment.mapping_quality)
self.assertEqual(
gaAlignment.alignment.position.referenceName,
readGroupInfo.samFile.getrname(pysamAlignment.reference_id))
self.assertEqual(gaAlignment.alignment.position.position,
pysamAlignment.reference_start)
# TODO test reverseStrand on position and on
# nextMatePosition once it has been implemented.
self.assertCigarEqual(gaAlignment.alignment.cigar,
pysamAlignment.cigar)
self.assertFlag(gaAlignment.duplicateFragment, pysamAlignment,
reads.SamFlags.DUPLICATE_READ)
self.assertFlag(gaAlignment.failedVendorQualityChecks, pysamAlignment,
reads.SamFlags.FAILED_QUALITY_CHECK)
self.assertEqual(gaAlignment.fragmentLength,
pysamAlignment.template_length)
self.assertEqual(gaAlignment.fragmentName, pysamAlignment.query_name)
compoundId = datamodel.ReadAlignmentCompoundId(
readGroupInfo.gaReadGroup.getCompoundId(),
pysamAlignment.query_name)
self.assertEqual(gaAlignment.id, str(compoundId))
self.assertEqual(
gaAlignment.info,
{key: [str(value)]
for key, value in pysamAlignment.tags})
if reads.SamFlags.isFlagSet(pysamAlignment.flag,
reads.SamFlags.MATE_UNMAPPED):
self.assertIsNone(gaAlignment.nextMatePosition)
else:
self.assertEqual(gaAlignment.nextMatePosition.position,
pysamAlignment.next_reference_start)
if pysamAlignment.next_reference_id != -1:
self.assertEqual(
gaAlignment.nextMatePosition.referenceName,
readGroupInfo.samFile.getrname(
pysamAlignment.next_reference_id))
else:
self.assertEqual(gaAlignment.nextMatePosition.referenceName,
"")
if gaAlignment.numberReads == 1:
self.assertFlag(False, pysamAlignment, reads.SamFlags.READ_PAIRED)
elif gaAlignment.numberReads == 2:
self.assertFlag(True, pysamAlignment, reads.SamFlags.READ_PAIRED)
else:
# we shouldn't be setting numberReads to anything else
self.assertTrue(False)
if gaAlignment.readNumber is None:
self.assertFlag(False, pysamAlignment,
reads.SamFlags.FIRST_IN_PAIR)
self.assertFlag(False, pysamAlignment,
reads.SamFlags.SECOND_IN_PAIR)
elif gaAlignment.readNumber == 0:
self.assertFlag(True, pysamAlignment, reads.SamFlags.FIRST_IN_PAIR)
self.assertFlag(False, pysamAlignment,
reads.SamFlags.SECOND_IN_PAIR)
elif gaAlignment.readNumber == 1:
self.assertFlag(False, pysamAlignment,
reads.SamFlags.FIRST_IN_PAIR)
self.assertFlag(True, pysamAlignment,
reads.SamFlags.SECOND_IN_PAIR)
elif gaAlignment.readNumber == 2:
self.assertFlag(True, pysamAlignment, reads.SamFlags.FIRST_IN_PAIR)
self.assertFlag(True, pysamAlignment,
reads.SamFlags.SECOND_IN_PAIR)
else:
# we shouldn't be setting readNumber to anything else
self.assertTrue(False)
self.assertFlag(gaAlignment.properPlacement, pysamAlignment,
reads.SamFlags.READ_PROPER_PAIR)
self.assertEqual(gaAlignment.readGroupId, readGroupInfo.id)
self.assertFlag(gaAlignment.secondaryAlignment, pysamAlignment,
reads.SamFlags.SECONDARY_ALIGNMENT)
self.assertFlag(gaAlignment.supplementaryAlignment, pysamAlignment,
reads.SamFlags.SUPPLEMENTARY_ALIGNMENT)
