def runCreateMultiCactusProject(expFile,
projectFile,
outgroupNames=None,
root=None,
overwrite=False):
options = CreateMultiCactusProjectOptions(expFile,
projectFile,
outgroupNames=outgroupNames,
root=root,
overwrite=overwrite)
expTemplate = ExperimentWrapper(ET.parse(options.expFile).getroot())
configPath = expTemplate.getConfigPath()
confTemplate = ConfigWrapper(ET.parse(configPath).getroot())
tree = expTemplate.getTree()
if options.outgroupNames is not None:
options.outgroupNames = set(options.outgroupNames)
projNames = set([tree.getName(x) for x in tree.getLeaves()])
for outgroupName in options.outgroupNames:
if outgroupName not in projNames:
raise RuntimeError("Specified outgroup %s not found in tree" %
outgroupName)
mcProj = createMCProject(tree, expTemplate, confTemplate, options)
expTemplate.setTree(mcProj.mcTree)
# Now do the file tree creation
createFileStructure(mcProj, expTemplate, confTemplate, options)
class TestCase(unittest.TestCase):
def setUp(self):
unittest.TestCase.setUp(self)
self.tree = NXNewick().parseString(
'((((HUMAN:0.006969,CHIMP:0.009727)anc2:0.025291,BABOON:0.044568)anc1:0.11,(MOUSE:0.072818,RAT:0.081244):0.260342):0.02326,((DOG:0.07,CAT:0.07):0.087381,(PIG:0.06,COW:0.06):0.104728):0.04);'
)
self.xmlRoot = self.__makeXmlDummy()
self.exp = ExperimentWrapper(self.xmlRoot)
self.exp.setTree(self.tree)
self.seqMap = {
'HUMAN': 'human.txt',
'CHIMP': 'chimp.txt',
'BABOON': 'baboon.txt',
'MOUSE': 'mouse.txt',
'RAT': 'rat.txt',
'DOG': 'dog.txt',
'CAT': 'cat.txt',
'PIG': 'pig.txt',
'COW': 'cow.txt'
}
self.exp.setRootGenome('anc1')
self.exp.setRootReconstructed(True)
self.exp.setOutgroupGenomes(
['MOUSE', 'RAT', 'DOG', 'CAT', 'PIG', 'COW'])
for genome, seq in self.seqMap.items():
# These aren't real IDs, but should still work for our
# purposes
self.exp.setSequenceID(genome, seq)
def testGetSequencePath(self):
for genome, seq in self.seqMap.items():
self.assertEqual(self.exp.getSequenceID(genome), seq)
# Should not be any entries for genomes not in the tree
self.assertEqual(self.exp.getSequenceID('DUCK'), None)
def testChangingSequencePaths(self):
"""Tests that changing a sequence path persists correctly."""
self.exp.setSequenceID('HUMAN', 'human2.txt')
self.assertEqual(self.exp.getSequenceID('HUMAN'), 'human2.txt')
# Reload the wrapper and try again
self.exp = ExperimentWrapper(self.xmlRoot)
self.assertEqual(self.exp.getSequenceID('HUMAN'), 'human2.txt')
def testOutgroups(self):
self.assertEqual(set(self.exp.getOutgroupGenomes()),
set(['MOUSE', 'RAT', 'DOG', 'CAT', 'PIG', 'COW']))
self.exp.setOutgroupGenomes([])
self.assertEqual(self.exp.getOutgroupGenomes(), [])
def testRootGenome(self):
self.assertEqual(self.exp.getRootGenome(), 'anc1')
self.exp.setRootGenome('anc2')
self.assertEqual(self.exp.getRootGenome(), 'anc2')
def testSetTree(self):
# A modfied version, with fewer genomes and a new one
tree2 = NXNewick().parseString(
'((HUMAN:0.006969,CHIMP:0.009727):0.025291,BABOON:0.044568,ARMADILLO:1.0);'
)
self.exp.setTree(tree2)
self.assertEqual(set(self.exp.getGenomesWithSequence()),
set(['HUMAN', 'CHIMP', 'BABOON']))
def __makeXmlDummy(self):
rootElem = ET.Element("dummy")
rootElem.append(self.__makeDiskElem())
return rootElem
def __makeDiskElem(self):
diskElem = ET.Element("cactus_disk")
confElem = ET.Element("st_kv_database_conf")
confElem.attrib['type'] = 'kyoto_tycoon'
diskElem.append(confElem)
dbElem = ET.Element('kyoto_tycoon')
confElem.append(dbElem)
return diskElem