class MultiCactusProject:
def __init__(self):
self.mcTree = None
self.expMap = dict()
self.expIDMap = None
self.inputSequences = []
self.inputSequenceIDs = None
self.outputSequenceIDMap = None
self.configID = None
def readXML(self, path):
xmlRoot = ET.parse(path).getroot()
treeElem = xmlRoot.find("tree")
self.mcTree = MultiCactusTree(NXNewick().parseString(
treeElem.text, addImpliedRoots=False))
self.expMap = dict()
self.expIDMap = dict()
cactusPathElemList = xmlRoot.findall("cactus")
for cactusPathElem in cactusPathElemList:
nameElem = cactusPathElem.attrib["name"]
pathElem = cactusPathElem.attrib["experiment_path"]
self.expMap[nameElem] = pathElem
if "experiment_id" in cactusPathElem.attrib:
self.expIDMap[nameElem] = cactusPathElem.attrib[
"experiment_id"]
self.inputSequences = xmlRoot.attrib["inputSequences"].split()
if "inputSequenceIDs" in xmlRoot.attrib:
self.inputSequenceIDs = xmlRoot.attrib["inputSequenceIDs"].split()
if "outputSequenceIDs" in xmlRoot.attrib:
self.outputSequenceIDMap = dict(
zip(xmlRoot.attrib["outputSequenceIDs"].split(),
xmlRoot.attrib["outputSequenceNames"].split()))
logger.info("xmlRoot = %s" % ET.tostring(xmlRoot))
if "configID" in xmlRoot.attrib:
self.configID = xmlRoot.attrib["configID"]
self.mcTree.assignSubtreeRootNames(self.expMap)
def writeXML(self, path):
xmlRoot = ET.Element("multi_cactus")
treeElem = ET.Element("tree")
treeElem.text = NXNewick().writeString(self.mcTree)
xmlRoot.append(treeElem)
for name, expPath in self.expMap.items():
cactusPathElem = ET.Element("cactus")
cactusPathElem.attrib["name"] = name
cactusPathElem.attrib["experiment_path"] = expPath
if self.expIDMap:
cactusPathElem.attrib["experiment_id"] = self.expIDMap[name]
xmlRoot.append(cactusPathElem)
#We keep track of all the input sequences at the top level
xmlRoot.attrib["inputSequences"] = " ".join(self.inputSequences)
if self.inputSequenceIDs:
xmlRoot.attrib["inputSequenceIDs"] = " ".join(
self.inputSequenceIDs)
if self.outputSequenceIDMap:
xmlRoot.attrib["outputSequenceIDs"] = " ".join(
self.outputSequenceIDMap.values())
xmlRoot.attrib["outputSequenceNames"] = " ".join(
self.outputSequenceIDMap.keys())
if self.configID:
xmlRoot.attrib["configID"] = self.configID
xmlFile = open(path, "w")
xmlString = ET.tostring(xmlRoot)
xmlString = minidom.parseString(xmlString).toprettyxml()
xmlFile.write(xmlString)
xmlFile.close()
def syncToFileStore(self, toil):
self.expIDMap = dict()
for name, expPath in self.expMap.items():
expWrapper = ExperimentWrapper(ET.parse(expPath).getroot())
expWrapper.setConfigID(
toil.importFile("file://" + expWrapper.getConfig()))
if expWrapper.getConstraintsFilePath():
expWrapper.setConstraintsID(
toil.importFile("file://" +
expWrapper.getConstraintsFilePath()))
expWrapper.writeXML(expPath)
self.expIDMap[name] = toil.importFile("file://" + expPath)
def getInputSequenceIDMap(self):
"""Return a map between event names and sequence IDs.
"""
inputSequenceMap = dict()
i = 0
for node in self.mcTree.postOrderTraversal():
if self.mcTree.isLeaf(node) is True:
inputSequenceMap[self.mcTree.getName(node)] = \
self.inputSequenceIDs[i]
i += 1
assert i == len(self.inputSequenceIDs)
return inputSequenceMap
def getInputSequenceIDs(self):
"""Get the set of input sequences for the multicactus tree
"""
return self.inputSequenceIDs
def getInputSequencePaths(self):
return self.inputSequences
def setOutputSequenceIDs(self, outputSequenceIDs):
self.outputSequenceIDMap = dict()
i = 0
for node in self.mcTree.postOrderTraversal():
if self.mcTree.isLeaf(node) is True:
self.outputSequenceIDMap[self.mcTree.getName(node)] = \
outputSequenceIDs[i]
i += 1
assert i == len(outputSequenceIDs)
def getOutputSequenceIDMap(self):
return self.outputSequenceIDMap
def getConfigPath(self):
return ExperimentWrapper(ET.parse(
self.expMap.values()[0]).getroot()).getConfigPath()
def setConfigID(self, configID):
self.configID = configID
def getConfigID(self):
return self.configID
def setInputSequenceIDs(self, inputSequenceIDs):
self.inputSequenceIDs = inputSequenceIDs
class MultiCactusProject:
def __init__(self):
self.mcTree = None
self.expMap = dict()
self.expIDMap = None
self.inputSequenceMap = {}
self.inputSequenceIDMap = {}
self.outputSequenceIDMap = {}
self.configID = None
def readXML(self, path):
xmlRoot = ET.parse(path).getroot()
treeElem = xmlRoot.find("tree")
self.mcTree = MultiCactusTree(NXNewick().parseString(
treeElem.text, addImpliedRoots=False))
self.expMap = dict()
self.expIDMap = dict()
cactusPathElemList = xmlRoot.findall("cactus")
for cactusPathElem in cactusPathElemList:
nameElem = cactusPathElem.attrib["name"]
pathElem = cactusPathElem.attrib["experiment_path"]
self.expMap[nameElem] = pathElem
if "experiment_id" in cactusPathElem.attrib:
self.expIDMap[nameElem] = cactusPathElem.attrib[
"experiment_id"]
self.inputSequenceMap = dict(
zip(xmlRoot.attrib["inputSequenceNames"].split(),
xmlRoot.attrib["inputSequences"].split()))
if "inputSequenceIDs" in xmlRoot.attrib:
self.inputSequenceIDMap = dict(
zip(xmlRoot.attrib["inputSequenceIDNames"].split(),
xmlRoot.attrib["inputSequenceIDs"].split()))
if "outputSequenceIDs" in xmlRoot.attrib:
self.outputSequenceIDMap = dict(
zip(xmlRoot.attrib["outputSequenceNames"].split(),
xmlRoot.attrib["outputSequenceIDs"].split()))
logger.info("xmlRoot = %s" % ET.tostring(xmlRoot))
if "configID" in xmlRoot.attrib:
self.configID = xmlRoot.attrib["configID"]
self.mcTree.assignSubtreeRootNames(self.expMap)
def writeXML(self, path):
xmlRoot = ET.Element("multi_cactus")
treeElem = ET.Element("tree")
treeElem.text = NXNewick().writeString(self.mcTree)
xmlRoot.append(treeElem)
for name, expPath in self.expMap.items():
cactusPathElem = ET.Element("cactus")
cactusPathElem.attrib["name"] = name
cactusPathElem.attrib["experiment_path"] = expPath
if self.expIDMap:
cactusPathElem.attrib["experiment_id"] = self.expIDMap[name]
xmlRoot.append(cactusPathElem)
#We keep track of all the input sequences at the top level
xmlRoot.attrib["inputSequences"] = " ".join(
self.inputSequenceMap.values())
xmlRoot.attrib["inputSequenceNames"] = " ".join(
self.inputSequenceMap.keys())
if self.inputSequenceIDMap:
xmlRoot.attrib["inputSequenceIDs"] = " ".join(
self.inputSequenceIDMap.values())
xmlRoot.attrib["inputSequenceIDNames"] = " ".join(
self.inputSequenceIDMap.keys())
if self.outputSequenceIDMap:
xmlRoot.attrib["outputSequenceIDs"] = " ".join(
self.outputSequenceIDMap.values())
xmlRoot.attrib["outputSequenceNames"] = " ".join(
self.outputSequenceIDMap.keys())
if self.configID:
xmlRoot.attrib["configID"] = self.configID
xmlFile = open(path, "w")
xmlString = ET.tostring(xmlRoot)
xmlString = minidom.parseString(xmlString).toprettyxml()
xmlFile.write(xmlString)
xmlFile.close()
def syncToFileStore(self, toil):
self.expIDMap = dict()
for name, expPath in self.expMap.items():
expWrapper = ExperimentWrapper(ET.parse(expPath).getroot())
expWrapper.setConfigID(
toil.importFile("file://" + expWrapper.getConfigPath()))
expWrapper.writeXML(expPath)
self.expIDMap[name] = toil.importFile("file://" + expPath)
def getConfigPath(self):
return ExperimentWrapper(ET.parse(
self.expMap.values()[0]).getroot()).getConfigPath()
def setConfigID(self, configID):
self.configID = configID
def getConfigID(self):
return self.configID
class MultiCactusProject:
def __init__(self):
self.mcTree = None
self.expMap = dict()
self.inputSequences = []
self.outputSequenceDir = None
def readXML(self, path):
xmlRoot = ET.parse(path).getroot()
treeElem = xmlRoot.find("tree")
self.mcTree = MultiCactusTree(NXNewick().parseString(treeElem.text, addImpliedRoots=False))
self.expMap = dict()
cactusPathElemList = xmlRoot.findall("cactus")
for cactusPathElem in cactusPathElemList:
nameElem = cactusPathElem.attrib["name"]
pathElem = cactusPathElem.attrib["experiment_path"]
self.expMap[nameElem] = pathElem
self.inputSequences = xmlRoot.attrib["inputSequences"].split()
self.outputSequenceDir = xmlRoot.attrib["outputSequenceDir"]
self.mcTree.assignSubtreeRootNames(self.expMap)
def writeXML(self, path):
xmlRoot = ET.Element("multi_cactus")
treeElem = ET.Element("tree")
treeElem.text = NXNewick().writeString(self.mcTree)
xmlRoot.append(treeElem)
for name, expPath in self.expMap.items():
cactusPathElem = ET.Element("cactus")
cactusPathElem.attrib["name"] = name
cactusPathElem.attrib["experiment_path"] = expPath
xmlRoot.append(cactusPathElem)
# We keep track of all the input sequences at the top level
xmlRoot.attrib["inputSequences"] = " ".join(self.inputSequences)
xmlRoot.attrib["outputSequenceDir"] = self.outputSequenceDir
xmlFile = open(path, "w")
xmlString = ET.tostring(xmlRoot)
xmlString = minidom.parseString(xmlString).toprettyxml()
xmlFile.write(xmlString)
xmlFile.close()
# find the sequence associated with an event name
# by digging out the appropriate experiment file
# doesn't work for the root!!!!
def sequencePath(self, eventName):
parentEvent = self.mcTree.getSubtreeRoot(eventName)
expPath = self.expMap[parentEvent]
expElem = ET.parse(expPath).getroot()
exp = ExperimentWrapper(expElem)
seq = exp.getSequence(eventName)
assert os.path.isfile(seq)
return seq
def getInputSequenceMap(self):
"""Return a map between event names and sequence paths. Paths
are different from above in that they are not taken from experiment
xmls, but rather from directly from the project xml.
"""
inputSequenceMap = dict()
i = 0
for node in self.mcTree.postOrderTraversal():
if self.mcTree.isLeaf(node) is True:
inputSequenceMap[self.mcTree.getName(node)] = self.inputSequences[i]
i += 1
assert i == len(self.inputSequences)
return inputSequenceMap
def getInputSequencePaths(self):
"""Get the set of input sequences for the multicactus tree
"""
return self.inputSequences
def getOutputSequenceDir(self):
"""The directory where the output sequences go
"""
return self.outputSequenceDir
def getConfigPath(self):
return ExperimentWrapper(ET.parse(self.expMap.values()[0]).getroot()).getConfigPath()
