def _parseTagValue(cls, value):
if len(value) > 1:
return [protocol.getValueFromValue(v) for v in value]
elif isinstance(
protocol.getValueFromValue(value[0]), (int, float, long)):
return protocol.getValueFromValue(value[0])
else:
return str(
protocol.getValueFromValue(value[0])).encode(cls._encoding)
def testGetValueFromValue(self):
with self.assertRaises(TypeError):
protocol.getValueFromValue(5)
val = common.AttributeValue()
with self.assertRaises(AttributeError):
protocol.getValueFromValue(val)
read = protocol.ReadAlignment()
expected = "1"
read.attributes.attr['key'].values.add().string_value = expected
tag, value = read.attributes.attr.items()[0]
result = protocol.getValueFromValue(value.values[0])
self.assertEquals(result, expected)
def testGetValueFromValue(self):
with self.assertRaises(TypeError):
protocol.getValueFromValue(5)
val = common.AttributeValue()
with self.assertRaises(AttributeError):
protocol.getValueFromValue(val)
read = protocol.ReadAlignment()
expected = "1"
read.attributes.attr['key'].values.add().string_value = expected
tag, value = read.attributes.attr.items()[0]
result = protocol.getValueFromValue(value.values[0])
self.assertEquals(result, expected)
def _parseTagValue(cls, tag, value):
if tag[0] in cls._tagReservedFieldPrefixes:
# user reserved fields... not really sure what to do here
return protocol.getValueFromValue(value.values[0]) \
.encode(cls._encoding)
elif tag in cls._tagIntegerFields:
return int(protocol.getValueFromValue(value.values[0]))
elif tag in cls._tagStringFields:
return protocol.getValueFromValue(value.values[0]) \
.encode(cls._encoding)
elif tag in cls._tagIntegerArrayFields:
return [int(integerString) for integerString in value]
else:
raise SamException("unrecognized tag '{}'".format(tag))
def _assertEquivalentGaVCFValues(gaValue, pyvcfValue):
compareValue = protocol.getValueFromValue(gaValue)
if isinstance(pyvcfValue, str):
self.assertEqual(compareValue, pyvcfValue)
elif isinstance(pyvcfValue, (int, bool)):
self.assertEqual(compareValue, pyvcfValue)
elif isinstance(pyvcfValue, float):
self.assertAlmostEqual(float(compareValue), float(pyvcfValue))
elif pyvcfValue is None:
self.assertEqual(compareValue, ".")
else:
raise Exception(key, (" values are inconsistent",
"between ga4ghObject and pyvcf!"))
def _assertEquivalentGaVCFValues(gaValue, pyvcfValue):
compareValue = protocol.getValueFromValue(gaValue)
if isinstance(pyvcfValue, str):
self.assertEqual(compareValue, pyvcfValue)
elif isinstance(pyvcfValue, (int, bool)):
self.assertEqual(compareValue, pyvcfValue)
elif isinstance(pyvcfValue, float):
self.assertAlmostEqual(float(compareValue), float(pyvcfValue))
elif pyvcfValue is None:
self.assertEqual(compareValue, ".")
else:
raise Exception(key, (
" values are inconsistent",
"between ga4ghObject and pyvcf!"))
def getDictFromMessageMap(self, messageMap):
return dict([(k, [protocol.getValueFromValue(x) for x in v.values])
for (k, v) in messageMap._values.items()])
def getDictFromMessageMap(self, messageMap):
return dict([
(k, [protocol.getValueFromValue(x) for x in v.values])
for (k, v) in messageMap._values.items()])