def run(self, fileStore):
self.configNode = ET.parse(fileStore.readGlobalFile(self.project.getConfigID())).getroot()
self.configWrapper = ConfigWrapper(self.configNode)
self.configWrapper.substituteAllPredefinedConstantsWithLiterals()
logger.info("Progressive Up: " + self.event)
# open up the experiment
# note that we copy the path into the options here
experimentFile = fileStore.readGlobalFile(self.project.expIDMap[self.event])
expXml = ET.parse(experimentFile).getroot()
experiment = ExperimentWrapper(expXml)
configPath = fileStore.readGlobalFile(experiment.getConfigID())
configXml = ET.parse(configPath).getroot()
seqIDMap = dict()
tree = experiment.getTree()
seqNames = []
for node in tree.postOrderTraversal():
if tree.isLeaf(node):
name = tree.getName(node)
seqIDMap[name] = self.project.outputSequenceIDMap[name]
seqNames.append(name)
logger.info("Sequences in progressive, %s: %s" % (self.event, seqNames))
experimentFile = fileStore.getLocalTempFile()
experiment.writeXML(experimentFile)
self.options.experimentFileID = fileStore.writeGlobalFile(experimentFile)
# take union of command line options and config options for hal and reference
if self.options.buildReference == False:
refNode = findRequiredNode(configXml, "reference")
self.options.buildReference = getOptionalAttrib(refNode, "buildReference", bool, False)
halNode = findRequiredNode(configXml, "hal")
if self.options.buildHal == False:
self.options.buildHal = getOptionalAttrib(halNode, "buildHal", bool, False)
if self.options.buildFasta == False:
self.options.buildFasta = getOptionalAttrib(halNode, "buildFasta", bool, False)
# get parameters that cactus_workflow stuff wants
configFile = fileStore.readGlobalFile(experiment.getConfigID())
configNode = ET.parse(configFile).getroot()
workFlowArgs = CactusWorkflowArguments(self.options, experimentFile=experimentFile, configNode=configNode, seqIDMap = seqIDMap)
# copy over the options so we don't trail them around
workFlowArgs.buildReference = self.options.buildReference
workFlowArgs.buildHal = self.options.buildHal
workFlowArgs.buildFasta = self.options.buildFasta
workFlowArgs.globalLeafEventSet = self.options.globalLeafEventSet
if self.options.intermediateResultsUrl is not None:
# Give the URL prefix a special name for this particular
# subproblem (by suffixing it with the name of the
# internal node in the guide tree)
workFlowArgs.intermediateResultsUrl = self.options.intermediateResultsUrl + '-' + self.event
# Use the trimming strategy to blast ingroups vs outgroups.
finalExpWrapper = self.addChild(CactusTrimmingBlastPhase(cactusWorkflowArguments=workFlowArgs, phaseName="trimBlast")).rv()
logger.info("Going to create alignments and define the cactus tree")
return finalExpWrapper
def run(self, fileStore):
self.configNode = ET.parse(fileStore.readGlobalFile(self.project.getConfigID())).getroot()
self.configWrapper = ConfigWrapper(self.configNode)
self.configWrapper.substituteAllPredefinedConstantsWithLiterals()
logger.info("Progressive Up: " + self.event)
# open up the experiment
# note that we copy the path into the options here
experimentFile = fileStore.readGlobalFile(self.project.expIDMap[self.event])
expXml = ET.parse(experimentFile).getroot()
experiment = ExperimentWrapper(expXml)
configPath = fileStore.readGlobalFile(experiment.getConfigID())
configXml = ET.parse(configPath).getroot()
seqIDMap = dict()
tree = experiment.getTree()
seqNames = []
for node in tree.postOrderTraversal():
if tree.isLeaf(node):
name = tree.getName(node)
seqIDMap[name] = self.project.outputSequenceIDMap[name]
seqNames.append(name)
logger.info("Sequences in progressive, %s: %s" % (self.event, seqNames))
experimentFile = fileStore.getLocalTempFile()
experiment.writeXML(experimentFile)
self.options.experimentFileID = fileStore.writeGlobalFile(experimentFile)
# take union of command line options and config options for hal and reference
if self.options.buildReference == False:
refNode = findRequiredNode(configXml, "reference")
self.options.buildReference = getOptionalAttrib(refNode, "buildReference", bool, False)
halNode = findRequiredNode(configXml, "hal")
if self.options.buildHal == False:
self.options.buildHal = getOptionalAttrib(halNode, "buildHal", bool, False)
if self.options.buildFasta == False:
self.options.buildFasta = getOptionalAttrib(halNode, "buildFasta", bool, False)
# get parameters that cactus_workflow stuff wants
configFile = fileStore.readGlobalFile(experiment.getConfigID())
configNode = ET.parse(configFile).getroot()
workFlowArgs = CactusWorkflowArguments(self.options, experimentFile=experimentFile, configNode=configNode, seqIDMap = seqIDMap)
# copy over the options so we don't trail them around
workFlowArgs.buildReference = self.options.buildReference
workFlowArgs.buildHal = self.options.buildHal
workFlowArgs.buildFasta = self.options.buildFasta
workFlowArgs.globalLeafEventSet = self.options.globalLeafEventSet
if self.options.intermediateResultsUrl is not None:
# Give the URL prefix a special name for this particular
# subproblem (by suffixing it with the name of the
# internal node in the guide tree)
workFlowArgs.intermediateResultsUrl = self.options.intermediateResultsUrl + '-' + self.event
# Use the trimming strategy to blast ingroups vs outgroups.
finalExpWrapper = self.addChild(CactusTrimmingBlastPhase(cactusWorkflowArguments=workFlowArgs, phaseName="trimBlast")).rv()
logger.info("Going to create alignments and define the cactus tree")
return finalExpWrapper
def exportHal(job, project, event=None, cacheBytes=None, cacheMDC=None, cacheRDC=None, cacheW0=None, chunk=None, deflate=None, inMemory=True,
checkpointInfo=None):
HALPath = "tmp_alignment.hal"
# traverse tree to make sure we are going breadth-first
tree = project.mcTree
# find subtree if event specified
rootNode = None
if event is not None:
assert event in tree.nameToId and not tree.isLeaf(tree.nameToId[event])
rootNode = tree.nameToId[event]
for node in tree.breadthFirstTraversal(rootNode):
genomeName = tree.getName(node)
if genomeName in project.expMap:
experimentFilePath = job.fileStore.readGlobalFile(project.expIDMap[genomeName])
experiment = ExperimentWrapper(ET.parse(experimentFilePath).getroot())
outgroups = experiment.getOutgroupGenomes()
experiment.setConfigPath(job.fileStore.readGlobalFile(experiment.getConfigID()))
expTreeString = NXNewick().writeString(experiment.getTree(onlyThisSubtree=True))
assert len(expTreeString) > 1
assert experiment.getHalID() is not None
assert experiment.getHalFastaID() is not None
subHALPath = job.fileStore.readGlobalFile(experiment.getHalID())
halFastaPath = job.fileStore.readGlobalFile(experiment.getHalFastaID())
args = [os.path.basename(subHALPath), os.path.basename(halFastaPath), expTreeString, os.path.basename(HALPath)]
if len(outgroups) > 0:
args += ["--outgroups", ",".join(outgroups)]
if cacheBytes is not None:
args += ["--cacheBytes", cacheBytes]
if cacheMDC is not None:
args += ["--cacheMDC", cacheMDC]
if cacheRDC is not None:
args += ["--cacheRDC", cacheRDC]
if cacheW0 is not None:
args += ["--cacheW0", cacheW0]
if chunk is not None:
args += ["--chunk", chunk]
if deflate is not None:
args += ["--deflate", deflate]
if inMemory is True:
args += ["--inMemory"]
cactus_call(parameters=["halAppendCactusSubtree"] + args)
cactus_call(parameters=["halSetMetadata", HALPath, "CACTUS_COMMIT", cactus_commit])
with job.fileStore.readGlobalFileStream(project.configID) as configFile:
cactus_call(parameters=["halSetMetadata", HALPath, "CACTUS_CONFIG", b64encode(configFile.read()).decode()])
if checkpointInfo:
write_s3(HALPath, checkpointInfo[1], region=checkpointInfo[0])
return job.fileStore.writeGlobalFile(HALPath)
def exportHal(job, project, event=None, cacheBytes=None, cacheMDC=None, cacheRDC=None, cacheW0=None, chunk=None, deflate=None, inMemory=False):
HALPath = "tmp_alignment.hal"
# traverse tree to make sure we are going breadth-first
tree = project.mcTree
# find subtree if event specified
rootNode = None
if event is not None:
assert event in tree.nameToId and not tree.isLeaf(tree.nameToId[event])
rootNode = tree.nameToId[event]
for node in tree.breadthFirstTraversal(rootNode):
genomeName = tree.getName(node)
if genomeName in project.expMap:
experimentFilePath = job.fileStore.readGlobalFile(project.expIDMap[genomeName])
experiment = ExperimentWrapper(ET.parse(experimentFilePath).getroot())
outgroups = experiment.getOutgroupEvents()
experiment.setConfigPath(job.fileStore.readGlobalFile(experiment.getConfigID()))
expTreeString = NXNewick().writeString(experiment.getTree(onlyThisSubtree=True))
assert len(expTreeString) > 1
assert experiment.getHalID() is not None
assert experiment.getHalFastaID() is not None
subHALPath = job.fileStore.readGlobalFile(experiment.getHalID())
halFastaPath = job.fileStore.readGlobalFile(experiment.getHalFastaID())
args = [os.path.basename(subHALPath), os.path.basename(halFastaPath), expTreeString, os.path.basename(HALPath)]
if len(outgroups) > 0:
args += ["--outgroups", ",".join(outgroups)]
if cacheBytes is not None:
args += ["--cacheBytes", cacheBytes]
if cacheMDC is not None:
args += ["--cacheMDC", cacheMDC]
if cacheRDC is not None:
args += ["--cacheRDC", cacheRDC]
if cacheW0 is not None:
args += ["--cacheW0", cacheW0]
if chunk is not None:
args += ["--chunk", chunk]
if deflate is not None:
args += ["--deflate", deflate]
if inMemory is True:
args += ["--inMemory"]
cactus_call(parameters=["halAppendCactusSubtree"] + args)
cactus_call(parameters=["halSetMetadata", HALPath, "CACTUS_COMMIT", cactus_commit])
with job.fileStore.readGlobalFileStream(project.configID) as configFile:
cactus_call(parameters=["halSetMetadata", HALPath, "CACTUS_CONFIG", b64encode(configFile.read())])
return job.fileStore.writeGlobalFile(HALPath)
def loadProject(self, mcProject, fileStore = None):
self.inGraph = NX.DiGraph()
globTree = mcProject.mcTree
self.maxParallelSubtrees = None
leafEvents = [globTree.getName(i) for i in globTree.getLeaves()]
expMap = None
if fileStore:
expMap = dict()
for name in mcProject.expIDMap:
expMap[name] = fileStore.readGlobalFile(mcProject.expIDMap[name])
else:
expMap = mcProject.expMap
for name, expPath in list(expMap.items()):
exp = ExperimentWrapper(ET.parse(expPath).getroot())
tree = exp.getTree()
self.inGraph.add_node(name)
# Go through the species tree and add the correct
# dependencies (i.e. to the outgroups and the ingroups,
# but not to the other nodes that are just there because
# they are needed to form the correct paths).
for node in tree.postOrderTraversal():
nodeName = tree.getName(node)
# we don't add edges for leaves (in the global tree)
# as they are input sequences and do not form dependencies
# (it would be clever to maybe do the same with existing
# references when --overwrite is not specified but for now
# we just do the leaves)
if nodeName not in leafEvents and tree.isLeaf(node):
self.inGraph.add_edge(name, nodeName)
if fileStore:
configFile = fileStore.readGlobalFile(exp.getConfigID())
else:
# hack from running from cactus-prepare
configFile = exp.getConfigPath()
configElem = ET.parse(configFile).getroot()
conf = ConfigWrapper(configElem)
# load max parellel subtrees from the node's config
if self.maxParallelSubtrees is None:
self.maxParallelSubtrees = conf.getMaxParallelSubtrees()
else:
assert self.maxParallelSubtrees == conf.getMaxParallelSubtrees()
assert NX.is_directed_acyclic_graph(self.inGraph)
def loadProject(self, mcProject, fileStore = None):
self.inGraph = NX.DiGraph()
globTree = mcProject.mcTree
self.maxParallelSubtrees = None
leafEvents = [globTree.getName(i) for i in globTree.getLeaves()]
expMap = None
if fileStore:
expMap = dict()
for name in mcProject.expIDMap:
expMap[name] = fileStore.readGlobalFile(mcProject.expIDMap[name])
else:
expMap = mcProject.expMap
for name, expPath in expMap.items():
exp = ExperimentWrapper(ET.parse(expPath).getroot())
tree = exp.getTree()
self.inGraph.add_node(name)
# Go through the species tree and add the correct
# dependencies (i.e. to the outgroups and the ingroups,
# but not to the other nodes that are just there because
# they are needed to form the correct paths).
for node in tree.postOrderTraversal():
nodeName = tree.getName(node)
# we don't add edges for leaves (in the global tree)
# as they are input sequences and do not form dependencies
# (it would be clever to maybe do the same with existing
# references when --overwrite is not specified but for now
# we just do the leaves)
if nodeName not in leafEvents and nodeName in exp.getSequenceMap():
self.inGraph.add_edge(name, nodeName)
configFile = fileStore.readGlobalFile(exp.getConfigID())
configElem = ET.parse(configFile).getroot()
conf = ConfigWrapper(configElem)
# load max parellel subtrees from the node's config
if self.maxParallelSubtrees is None:
self.maxParallelSubtrees = conf.getMaxParallelSubtrees()
else:
assert self.maxParallelSubtrees == conf.getMaxParallelSubtrees()
assert NX.is_directed_acyclic_graph(self.inGraph)
