def _createReadAlignment(self, i, seed):
# TODO fill out a bit more
rng = random.Random(seed)
alignment = protocol.ReadAlignment()
alignment.fragmentLength = rng.randint(10, 100)
alignment.alignedQuality = []
alignment.alignedSequence = ""
for i in range(alignment.fragmentLength):
# TODO: are these reasonable quality values?
alignment.alignedQuality.append(rng.randint(1, 20))
alignment.alignedSequence += rng.choice("ACGT")
alignment.fragmentId = "frag{}".format(seed)
gaPosition = protocol.Position()
gaPosition.position = 0
gaPosition.referenceName = "NotImplemented"
gaPosition.strand = protocol.Strand.POS_STRAND
gaLinearAlignment = protocol.LinearAlignment()
gaLinearAlignment.position = gaPosition
alignment.alignment = gaLinearAlignment
alignment.duplicateFragment = False
alignment.failedVendorQualityChecks = False
alignment.fragmentName = "simulated{}".format(i)
alignment.info = {}
alignment.nextMatePosition = None
alignment.numberReads = None
alignment.properPlacement = False
alignment.readGroupId = self.getId()
alignment.readNumber = None
alignment.secondaryAlignment = False
alignment.supplementaryAlignment = False
alignment.id = self.getReadAlignmentId(alignment)
return alignment
def generateReadAlignment(position=0, sequence='abc'):
alignment = protocol.ReadAlignment()
alignment.alignment = protocol.LinearAlignment()
alignment.alignment.position = protocol.Position()
alignment.alignment.position.position = position
alignment.alignedSequence = sequence
return alignment
def _createReadAlignment(self, i):
# TODO fill out a bit more
alignment = protocol.ReadAlignment()
alignment.alignedQuality = [1, 2, 3]
alignment.alignedSequence = "ACT"
alignment.fragmentId = 'TODO'
gaPosition = protocol.Position()
gaPosition.position = 0
gaPosition.referenceName = "NotImplemented"
gaPosition.strand = protocol.Strand.POS_STRAND
gaLinearAlignment = protocol.LinearAlignment()
gaLinearAlignment.position = gaPosition
alignment.alignment = gaLinearAlignment
alignment.duplicateFragment = False
alignment.failedVendorQualityChecks = False
alignment.fragmentLength = 3
alignment.fragmentName = "simulated{}".format(i)
alignment.info = {}
alignment.nextMatePosition = None
alignment.numberReads = None
alignment.properPlacement = False
alignment.readGroupId = self.getId()
alignment.readNumber = None
alignment.secondaryAlignment = False
alignment.supplementaryAlignment = False
alignment.id = self.getReadAlignmentId(alignment)
return alignment
def _createReadAlignment(self, i, seed):
# TODO fill out a bit more
rng = random.Random(seed)
alignment = protocol.ReadAlignment()
alignment.fragment_length = rng.randint(10, 100)
alignment.aligned_sequence = ""
for i in range(alignment.fragment_length):
# TODO: are these reasonable quality values?
alignment.aligned_quality.append(rng.randint(1, 20))
alignment.aligned_sequence += rng.choice("ACGT")
alignment.alignment.position.position = 0
alignment.alignment.position.reference_name = "NotImplemented"
alignment.alignment.position.strand = protocol.POS_STRAND
alignment.duplicate_fragment = False
alignment.failed_vendor_quality_checks = False
alignment.fragment_name = "{}$simulated{}".format(
self.getLocalId(), i)
alignment.number_reads = 0
alignment.improper_placement = False
alignment.read_group_id = self.getId()
alignment.read_number = -1
alignment.secondary_alignment = False
alignment.supplementary_alignment = False
alignment.id = self._parentContainer.getReadAlignmentId(alignment)
return alignment
def testInstantiation(self):
for class_ in self._getExceptionClasses():
# some exceptions are becoming too complicated to instantiate
# like the rest of the exceptions; just do them manually
if class_ == exceptions.RequestValidationFailureException:
wrongString = "thisIsWrong"
objClass = protocol.SearchReadsRequest
obj = objClass()
obj.start = wrongString
jsonDict = obj.toJsonDict()
args = (jsonDict, objClass)
elif class_ == exceptions.ResponseValidationFailureException:
objClass = protocol.SearchReadsResponse
obj = objClass()
obj.alignments = [protocol.ReadAlignment()]
obj.alignments[0].alignment = protocol.LinearAlignment()
obj.alignments[0].alignment.mappingQuality = wrongString
jsonDict = obj.toJsonDict()
args = (jsonDict, objClass)
else:
numInitArgs = len(inspect.getargspec(class_.__init__).args) - 1
args = ['arg' for _ in range(numInitArgs)]
instance = class_(*args)
self.assertIsInstance(instance, exceptions.BaseServerException)
message = instance.getMessage()
self.assertIsInstance(message, basestring)
self.assertGreater(len(message), 0)
self.assertEqual(instance.getErrorCode(), class_.getErrorCode())
def convertReadAlignment(self, read):
"""
Convert a pysam ReadAlignment to a GA4GH ReadAlignment
"""
# TODO fill out remaining fields
# TODO refine in tandem with code in converters module
ret = protocol.ReadAlignment()
ret.alignedQuality = list(read.query_qualities)
ret.alignedSequence = read.query_sequence
ret.alignment = protocol.LinearAlignment()
ret.alignment.mappingQuality = read.mapping_quality
ret.alignment.position = protocol.Position()
ret.alignment.position.referenceName = self._samFile.getrname(
read.reference_id)
ret.alignment.position.position = read.reference_start
ret.alignment.position.strand = \
protocol.Strand.POS_STRAND # TODO fix this!
ret.alignment.cigar = []
for operation, length in read.cigar:
gaCigarUnit = protocol.CigarUnit()
gaCigarUnit.operation = SamCigar.int2ga(operation)
gaCigarUnit.operationLength = length
gaCigarUnit.referenceSequence = None # TODO fix this!
ret.alignment.cigar.append(gaCigarUnit)
ret.duplicateFragment = SamFlags.isFlagSet(read.flag,
SamFlags.DUPLICATE_FRAGMENT)
ret.failedVendorQualityChecks = SamFlags.isFlagSet(
read.flag, SamFlags.FAILED_VENDOR_QUALITY_CHECKS)
ret.fragmentLength = read.template_length
ret.fragmentName = read.query_name
ret.id = "{}:{}".format(self._id, read.query_name)
ret.info = {key: [str(value)] for key, value in read.tags}
ret.nextMatePosition = None
if read.next_reference_id != -1:
ret.nextMatePosition = protocol.Position()
ret.nextMatePosition.referenceName = self._samFile.getrname(
read.next_reference_id)
ret.nextMatePosition.position = read.next_reference_start
ret.nextMatePosition.strand = \
protocol.Strand.POS_STRAND # TODO fix this!
# TODO Is this the correct mapping between numberReads and
# sam flag 0x1? What about the mapping between numberReads
# and 0x40 and 0x80?
ret.numberReads = None
ret.readNumber = None
if SamFlags.isFlagSet(read.flag, SamFlags.NUMBER_READS):
ret.numberReads = 2
if SamFlags.isFlagSet(read.flag, SamFlags.READ_NUMBER_ONE):
ret.readNumber = 0
elif SamFlags.isFlagSet(read.flag, SamFlags.READ_NUMBER_TWO):
ret.readNumber = 1
ret.properPlacement = SamFlags.isFlagSet(read.flag,
SamFlags.PROPER_PLACEMENT)
ret.readGroupId = self._id
ret.secondaryAlignment = SamFlags.isFlagSet(
read.flag, SamFlags.SECONDARY_ALIGNMENT)
ret.supplementaryAlignment = SamFlags.isFlagSet(
read.flag, SamFlags.SUPPLEMENTARY_ALIGNMENT)
return ret
def testValidationFailureExceptionMessages(self):
# RequestValidationFailureException
wrongString = "thisIsWrong"
objClass = protocol.SearchReadsRequest
obj = objClass()
obj.start = wrongString
jsonDict = obj.toJsonDict()
instance = exceptions.RequestValidationFailureException(
jsonDict, objClass)
self.assertIn("invalid fields:", instance.message)
self.assertIn("u'start': u'thisIsWrong'", instance.message)
self.assertEqual(instance.message.count(wrongString), 2)
# ResponseValidationFailureException
objClass = protocol.SearchReadsResponse
obj = objClass()
obj.alignments.extend([protocol.ReadAlignment()])
obj.alignments[0].alignment.mapping_quality = wrongString
jsonDict = obj.toJsonDict()
instance = exceptions.ResponseValidationFailureException(
jsonDict, objClass)
self.assertIn("Invalid fields", instance.message)
self.assertEqual(instance.message.count(wrongString), 2)
def convertReadAlignment(self, read):
"""
Convert a pysam ReadAlignment to a GA4GH ReadAlignment
"""
samFile = self._parentContainer.getFileHandle(self._parentSamFilePath)
# TODO fill out remaining fields
# TODO refine in tandem with code in converters module
ret = protocol.ReadAlignment()
ret.fragmentId = 'TODO'
if read.query_qualities is None:
ret.alignedQuality = []
else:
ret.alignedQuality = list(read.query_qualities)
ret.alignedSequence = read.query_sequence
if SamFlags.isFlagSet(read.flag, SamFlags.READ_UNMAPPED):
ret.alignment = None
else:
ret.alignment = protocol.LinearAlignment()
ret.alignment.mappingQuality = read.mapping_quality
ret.alignment.position = protocol.Position()
ret.alignment.position.referenceName = samFile.getrname(
read.reference_id)
ret.alignment.position.position = read.reference_start
ret.alignment.position.strand = protocol.Strand.POS_STRAND
if SamFlags.isFlagSet(read.flag, SamFlags.READ_REVERSE_STRAND):
ret.alignment.position.strand = protocol.Strand.NEG_STRAND
ret.alignment.cigar = []
for operation, length in read.cigar:
gaCigarUnit = protocol.CigarUnit()
gaCigarUnit.operation = SamCigar.int2ga(operation)
gaCigarUnit.operationLength = length
gaCigarUnit.referenceSequence = None # TODO fix this!
ret.alignment.cigar.append(gaCigarUnit)
ret.duplicateFragment = SamFlags.isFlagSet(read.flag,
SamFlags.DUPLICATE_READ)
ret.failedVendorQualityChecks = SamFlags.isFlagSet(
read.flag, SamFlags.FAILED_QUALITY_CHECK)
ret.fragmentLength = read.template_length
ret.fragmentName = read.query_name
ret.info = {key: [str(value)] for key, value in read.tags}
if SamFlags.isFlagSet(read.flag, SamFlags.MATE_UNMAPPED):
ret.nextMatePosition = None
else:
ret.nextMatePosition = protocol.Position()
if read.next_reference_id != -1:
ret.nextMatePosition.referenceName = samFile.getrname(
read.next_reference_id)
else:
ret.nextMatePosition.referenceName = ""
ret.nextMatePosition.position = read.next_reference_start
ret.nextMatePosition.strand = protocol.Strand.POS_STRAND
if SamFlags.isFlagSet(read.flag, SamFlags.MATE_REVERSE_STRAND):
ret.nextMatePosition.strand = protocol.Strand.NEG_STRAND
if SamFlags.isFlagSet(read.flag, SamFlags.READ_PAIRED):
ret.numberReads = 2
else:
ret.numberReads = 1
ret.readNumber = None
if SamFlags.isFlagSet(read.flag, SamFlags.FIRST_IN_PAIR):
if SamFlags.isFlagSet(read.flag, SamFlags.SECOND_IN_PAIR):
ret.readNumber = 2
else:
ret.readNumber = 0
elif SamFlags.isFlagSet(read.flag, SamFlags.SECOND_IN_PAIR):
ret.readNumber = 1
ret.properPlacement = SamFlags.isFlagSet(read.flag,
SamFlags.READ_PROPER_PAIR)
ret.readGroupId = self.getId()
ret.secondaryAlignment = SamFlags.isFlagSet(
read.flag, SamFlags.SECONDARY_ALIGNMENT)
ret.supplementaryAlignment = SamFlags.isFlagSet(
read.flag, SamFlags.SUPPLEMENTARY_ALIGNMENT)
ret.id = self.getReadAlignmentId(ret)
return ret
def convertReadAlignment(self, read, readGroupSet, readGroupId):
"""
Convert a pysam ReadAlignment to a GA4GH ReadAlignment
"""
samFile = self.getFileHandle(self._dataUrl)
# TODO fill out remaining fields
# TODO refine in tandem with code in converters module
ret = protocol.ReadAlignment()
# ret.fragmentId = 'TODO'
ret.aligned_quality.extend(read.query_qualities)
ret.aligned_sequence = read.query_sequence
if SamFlags.isFlagSet(read.flag, SamFlags.READ_UNMAPPED):
ret.ClearField("alignment")
else:
ret.alignment.CopyFrom(protocol.LinearAlignment())
ret.alignment.mapping_quality = read.mapping_quality
ret.alignment.position.CopyFrom(protocol.Position())
ret.alignment.position.reference_name = samFile.getrname(
read.reference_id)
ret.alignment.position.position = read.reference_start
ret.alignment.position.strand = protocol.POS_STRAND
if SamFlags.isFlagSet(read.flag, SamFlags.READ_REVERSE_STRAND):
ret.alignment.position.strand = protocol.NEG_STRAND
for operation, length in read.cigar:
gaCigarUnit = ret.alignment.cigar.add()
gaCigarUnit.operation = SamCigar.int2ga(operation)
gaCigarUnit.operation_length = length
gaCigarUnit.reference_sequence = "" # TODO fix this!
ret.duplicate_fragment = SamFlags.isFlagSet(
read.flag, SamFlags.DUPLICATE_READ)
ret.failed_vendor_quality_checks = SamFlags.isFlagSet(
read.flag, SamFlags.FAILED_QUALITY_CHECK)
ret.fragment_length = read.template_length
ret.fragment_name = read.query_name
for key, value in read.tags:
ret.info[key].values.add().string_value = str(value)
if SamFlags.isFlagSet(read.flag, SamFlags.MATE_UNMAPPED):
ret.next_mate_position.Clear()
else:
ret.next_mate_position.Clear()
if read.next_reference_id != -1:
ret.next_mate_position.reference_name = samFile.getrname(
read.next_reference_id)
else:
ret.next_mate_position.reference_name = ""
ret.next_mate_position.position = read.next_reference_start
ret.next_mate_position.strand = protocol.POS_STRAND
if SamFlags.isFlagSet(read.flag, SamFlags.MATE_REVERSE_STRAND):
ret.next_mate_position.strand = protocol.NEG_STRAND
if SamFlags.isFlagSet(read.flag, SamFlags.READ_PAIRED):
ret.number_reads = 2
else:
ret.number_reads = 1
ret.read_number = -1
if SamFlags.isFlagSet(read.flag, SamFlags.FIRST_IN_PAIR):
if SamFlags.isFlagSet(read.flag, SamFlags.SECOND_IN_PAIR):
ret.read_number = 2
else:
ret.read_number = 0
elif SamFlags.isFlagSet(read.flag, SamFlags.SECOND_IN_PAIR):
ret.read_number = 1
ret.improper_placement = not SamFlags.isFlagSet(
read.flag, SamFlags.READ_PROPER_PAIR)
ret.read_group_id = readGroupId
ret.secondary_alignment = SamFlags.isFlagSet(
read.flag, SamFlags.SECONDARY_ALIGNMENT)
ret.supplementary_alignment = SamFlags.isFlagSet(
read.flag, SamFlags.SUPPLEMENTARY_ALIGNMENT)
ret.id = readGroupSet.getReadAlignmentId(ret)
return ret
