def testChainLength(self):
"""
Passing a chain length to toString must result in the expected XML.
"""
xml = BEAST2XML(clockModel=self.CLOCK_MODEL)
tree = ET.ElementTree(ET.fromstring(xml.toString(chainLength=100)))
elements = BEAST2XML.findElements(tree)
self.assertEqual('100', elements['run'].get('chainLength'))
def testDateUnit(self):
"""
Passing a dateUnit value to toString must result in the expected XML.
"""
xml = BEAST2XML(clockModel=self.CLOCK_MODEL)
tree = ET.ElementTree(ET.fromstring(xml.toString(dateUnit='day')))
elements = BEAST2XML.findElements(tree)
trait = elements['./run/state/tree/trait']
self.assertEqual('day', trait.get('units'))
def testNoDateUnit(self):
"""
Passing no dateUnit value to toString must result in the expected XML
(with no 'units' attribute in the trait).
"""
xml = BEAST2XML(clockModel=self.CLOCK_MODEL)
tree = ET.ElementTree(ET.fromstring(xml.toString()))
elements = BEAST2XML.findElements(tree)
trait = elements['./run/state/tree/trait']
self.assertEqual(None, trait.get('units'))
def testDefaultDateDirection(self):
"""
Passing no dateDirection toString must result in the expected date
direction in the XML.
"""
xml = BEAST2XML(clockModel=self.CLOCK_MODEL)
tree = ET.ElementTree(ET.fromstring(xml.toString()))
elements = BEAST2XML.findElements(tree)
trait = elements['./run/state/tree/trait']
self.assertEqual('date-backward', trait.get('traitname'))
def testScreenLogEvery(self):
"""
Passing a screenLogEvery value to toString must result in the expected
XML.
"""
xml = BEAST2XML(clockModel=self.CLOCK_MODEL)
tree = ET.ElementTree(ET.fromstring(xml.toString(screenLogEvery=300)))
elements = BEAST2XML.findElements(tree)
logger = elements["./run/logger[@id='screenlog']"]
self.assertEqual('300', logger.get('logEvery'))
def testDefaultAge(self):
"""
Passing a default age to toString must result in the expected XML.
"""
xml = BEAST2XML(clockModel=self.CLOCK_MODEL)
xml.addSequence(Read('id1', 'ACTG'))
tree = ET.ElementTree(ET.fromstring(xml.toString(defaultAge=33.0)))
elements = BEAST2XML.findElements(tree)
# The sequence id with the default age of 0.0 must be in the traits.
trait = elements['./run/state/tree/trait']
self.assertTrue(trait.text.find('id1=33.0') > -1)
def testOneSequenceWithAgeAddedTogether(self):
"""
Adding a sequence with an age (both passed to addSequence) must result
in the expected XML.
"""
xml = BEAST2XML(clockModel=self.CLOCK_MODEL)
xml.addSequence(Read('id1', 'ACTG'), 44)
tree = ET.ElementTree(ET.fromstring(xml.toString()))
elements = BEAST2XML.findElements(tree)
# The sequence id with the given age must be in the traits.
trait = elements['./run/state/tree/trait']
self.assertTrue(trait.text.find('id1=44.0') > -1)
def testSequenceIdDateRegex(self):
"""
Using a sequence id date regex must result in the expected XML.
"""
xml = BEAST2XML(clockModel=self.CLOCK_MODEL,
sequenceIdDateRegex='^.*_([0-9]+)')
xml.addSequence(Read('id1_80_xxx', 'ACTG'))
tree = ET.ElementTree(ET.fromstring(xml.toString()))
elements = BEAST2XML.findElements(tree)
# The sequence id with the default age of 0.0 must be in the traits.
trait = elements['./run/state/tree/trait']
self.assertTrue(trait.text.find('id1_80_xxx=80.0') > -1)
def testSequenceIdDateRegexNonMatchingNotAnError(self):
"""
Using a sequence id date regex that doesn't match is not an error if
we pass sequenceIdDateRegexMayNotMatch=True, in which case the default
age should be assigned.
"""
xml = BEAST2XML(clockModel=self.CLOCK_MODEL,
sequenceIdDateRegex='^.*_([0-9]+)',
sequenceIdDateRegexMayNotMatch=True)
xml.addSequence(Read('id1_xxx', 'ACTG'))
tree = ET.ElementTree(ET.fromstring(xml.toString(defaultAge=50)))
elements = BEAST2XML.findElements(tree)
# The sequence id with the passed default age must be in the traits.
trait = elements['./run/state/tree/trait']
self.assertTrue(trait.text.find('id1_xxx=50.0') > -1)
def testLogFileBaseName(self):
"""
Passing a log file base name to toString must result in the expected
log file names in the XML.
"""
xml = BEAST2XML(clockModel=self.CLOCK_MODEL)
tree = ET.ElementTree(
ET.fromstring(xml.toString(logFileBasename='xxx')))
elements = BEAST2XML.findElements(tree)
logger = elements["./run/logger[@id='tracelog']"]
self.assertEqual('xxx' + BEAST2XML.TRACELOG_SUFFIX,
logger.get('fileName'))
logger = elements["./run/logger[@id='treelog.t:alignment']"]
self.assertEqual('xxx' + BEAST2XML.TREELOG_SUFFIX,
logger.get('fileName'))
def testAddSequences(self):
"""
Adding several sequences must result in the expected XML.
"""
xml = BEAST2XML(clockModel=self.CLOCK_MODEL)
xml.addSequences(
[Read('id1', 'GG'),
Read('id2', 'CC'),
Read('id3', 'AA')])
tree = ET.ElementTree(ET.fromstring(xml.toString()))
elements = BEAST2XML.findElements(tree)
# The sequences must be the children of the <data> tag.
data = elements['data']
self.assertEqual(3, len(data))
child = data[0]
self.assertEqual('sequence', child.tag)
self.assertEqual('GG', child.get('value'))
self.assertEqual('4', child.get('totalcount'))
self.assertEqual('id1', child.get('taxon'))
self.assertEqual('seq_id1', child.get('id'))
self.assertIs(None, child.text)
child = data[1]
self.assertEqual('sequence', child.tag)
self.assertEqual('CC', child.get('value'))
self.assertEqual('4', child.get('totalcount'))
self.assertEqual('id2', child.get('taxon'))
self.assertEqual('seq_id2', child.get('id'))
self.assertIs(None, child.text)
child = data[2]
self.assertEqual('sequence', child.tag)
self.assertEqual('AA', child.get('value'))
self.assertEqual('4', child.get('totalcount'))
self.assertEqual('id3', child.get('taxon'))
self.assertEqual('seq_id3', child.get('id'))
self.assertIs(None, child.text)
# The sequence ids with the default age of 0.0 must be in the traits.
trait = elements['./run/state/tree/trait']
self.assertTrue(trait.text.find('id1=0.0') > -1)
self.assertTrue(trait.text.find('id2=0.0') > -1)
self.assertTrue(trait.text.find('id3=0.0') > -1)
def testOneSequenceWithDateRegexAndDateUnitInDays(self):
"""
Adding a sequence with a date regex and date units in days must
result in the expected XML.
"""
sequenceDate = (date.today() - timedelta(days=10)).strftime('%Y-%m-%d')
r = r'^.*_(?P<year>\d\d\d\d)-(?P<month>\d\d)-(?P<day>\d\d)'
id_ = 'id1_' + sequenceDate
xml = BEAST2XML(clockModel=self.CLOCK_MODEL,
sequenceIdDateRegex=r,
dateUnit='day')
xml.addSequence(Read(id_, 'ACTG'))
tree = ET.ElementTree(ET.fromstring(xml.toString()))
elements = BEAST2XML.findElements(tree)
# The sequence id with an age of 10 days must be in the traits.
trait = elements['./run/state/tree/trait']
self.assertTrue(trait.text.find(id_ + '=10.0') > -1)
self.assertEqual('day', trait.get('units'))
def testOneSequence(self):
"""
Adding a sequence must result in the expected XML.
"""
xml = BEAST2XML(clockModel=self.CLOCK_MODEL)
xml.addSequence(Read('id1', 'ACTG'))
tree = ET.ElementTree(ET.fromstring(xml.toString()))
elements = BEAST2XML.findElements(tree)
# The sequence must be the only child of the <data> tag.
data = elements['data']
self.assertEqual(1, len(data))
child = data[0]
self.assertEqual('sequence', child.tag)
self.assertEqual('ACTG', child.get('value'))
self.assertEqual('4', child.get('totalcount'))
self.assertEqual('id1', child.get('taxon'))
self.assertEqual('seq_id1', child.get('id'))
self.assertIs(None, child.text)
# The sequence id with the default age of 0.0 must be in the traits.
trait = elements['./run/state/tree/trait']
self.assertTrue(trait.text.find('id1=0.0') > -1)