def __init__(self, options):
self.options = options
self.seqFile = SeqFile(options.seqFile)
self.workingDir = options.cactusDir
self.configWrapper = None
self.expWrapper = None
self.processConfig()
self.processExperiment()
class ProjectWrapper:
alignmentDirName = 'progressiveAlignment'
def __init__(self, options):
self.options = options
self.seqFile = SeqFile(options.seqFile)
self.workingDir = options.cactusDir
self.configWrapper = None
self.expWrapper = None
self.processConfig()
self.processExperiment()
def processConfig(self):
# read in the default right out of cactus
if self.options.configFile is not None:
configPath = self.options.configFile
else:
dir = cactusRootPath()
configPath = os.path.join(dir, "cactus_progressive_config.xml")
log.info("Using config from path %s." % configPath)
configXml = ET.parse(configPath).getroot()
self.configWrapper = ConfigWrapper(configXml)
# here we can go through the options and apply some to the config
self.configWrapper.setBuildHal(True)
self.configWrapper.setBuildFasta(True)
def processExperiment(self):
expXml = self.seqFile.toXMLElement()
#create the cactus disk
cdElem = ET.SubElement(expXml, "cactus_disk")
database = self.options.database
assert database == "kyoto_tycoon" or database == "tokyo_cabinet"
confElem = ET.SubElement(cdElem, "st_kv_database_conf")
confElem.attrib["type"] = database
ET.SubElement(confElem, database)
self.expWrapper = ExperimentWrapper(expXml)
if not os.path.exists(self.workingDir):
os.makedirs(self.workingDir)
def writeXml(self):
assert os.path.isdir(self.workingDir)
configPath = absSymPath(os.path.join(self.workingDir, "config.xml"))
expPath = absSymPath(os.path.join(self.workingDir, "expTemplate.xml"))
self.expWrapper.setConfigPath(configPath)
self.configWrapper.writeXML(configPath)
self.expWrapper.writeXML(expPath)
projPath = os.path.join(self.workingDir,
ProjectWrapper.alignmentDirName)
if len(self.seqFile.outgroups) == 0:
# No outgroups specified, assume the default outgroup set
outgroups = None
else:
outgroups = self.seqFile.outgroups
runCreateMultiCactusProject(expPath,
projPath,
fixNames=0,
outgroupNames=outgroups,
root=self.options.root)
class ProjectWrapper:
alignmentDirName = 'progressiveAlignment'
def __init__(self, options):
self.options = options
self.seqFile = SeqFile(options.seqFile)
self.workingDir = options.cactusDir
self.configWrapper = None
self.expWrapper = None
self.processConfig()
self.processExperiment()
def processConfig(self):
# read in the default right out of cactus
if self.options.configFile is not None:
configPath = self.options.configFile
else:
dir = cactusRootPath()
configPath = os.path.join(dir,
"cactus_progressive_config.xml")
log.info("Using config from path %s." % configPath)
configXml = ET.parse(configPath).getroot()
self.configWrapper = ConfigWrapper(configXml)
# here we can go through the options and apply some to the config
self.configWrapper.setBuildHal(True)
self.configWrapper.setBuildFasta(True)
def processExperiment(self):
expXml = self.seqFile.toXMLElement()
#create the cactus disk
cdElem = ET.SubElement(expXml, "cactus_disk")
database = self.options.database
assert database == "kyoto_tycoon" or database == "tokyo_cabinet"
confElem = ET.SubElement(cdElem, "st_kv_database_conf")
confElem.attrib["type"] = database
ET.SubElement(confElem, database)
self.expWrapper = ExperimentWrapper(expXml)
if not os.path.exists(self.workingDir):
os.makedirs(self.workingDir)
def writeXml(self):
assert os.path.isdir(self.workingDir)
configPath = absSymPath(
os.path.join(self.workingDir, "config.xml"))
expPath = absSymPath(
os.path.join(self.workingDir, "expTemplate.xml"))
self.expWrapper.setConfigPath(configPath)
self.configWrapper.writeXML(configPath)
self.expWrapper.writeXML(expPath)
projPath = os.path.join(self.workingDir,
ProjectWrapper.alignmentDirName)
if len(self.seqFile.outgroups) == 0:
# No outgroups specified, assume the default outgroup set
outgroups = None
else:
outgroups = self.seqFile.outgroups
runCreateMultiCactusProject(expPath, projPath, fixNames=0,
outgroupNames=outgroups,
root=self.options.root)
def __init__(self, options):
self.options = options
self.seqFile = SeqFile(options.seqFile)
self.workingDir = options.cactusDir
self.configWrapper = None
self.expWrapper = None
self.processConfig()
self.processExperiment()
def main():
# init as dummy function
cleanKtFn = lambda x,y:x
stage = -1
workDir = None
try:
parser = initParser()
options, args = parser.parse_args()
if (options.rootOutgroupDists is not None) \
^ (options.rootOutgroupPaths is not None):
parser.error("--rootOutgroupDists and --rootOutgroupPaths must be " +
"provided together")
if len(args) == 0:
parser.print_help()
return 1
if len(args) != 3:
raise RuntimeError("Error parsing command line. Exactly 3 arguments are required but %d arguments were detected: %s" % (len(args), str(args)))
if options.optionsFile != None:
fileArgs = parseOptionsFile(options.optionsFile)
options, args = parser.parse_args(fileArgs + sys.argv[1:])
if len(args) != 3:
raise RuntimeError("Error parsing options file. Make sure all "
"options have -- prefix")
stage = 0
setLoggingFromOptions(options)
seqFile = SeqFile(args[0])
workDir = args[1]
outputHalFile = args[2]
validateInput(workDir, outputHalFile, options)
jtPath = os.path.join(workDir, "jobTree")
stage = 1
print "\nBeginning Alignment"
system("rm -rf %s" % jtPath)
projWrapper = ProjectWrapper(options, seqFile, workDir)
projWrapper.writeXml()
jtCommands = getJobTreeCommands(jtPath, parser, options)
runCactus(workDir, jtCommands, jtPath, options)
cmd = 'jobTreeStatus --failIfNotComplete --jobTree %s > /dev/null 2>&1 ' %\
jtPath
system(cmd)
stage = 2
print "Beginning HAL Export"
extractOutput(workDir, outputHalFile, options)
print "Success.\n" "Temporary data was left in: %s\n" \
% workDir
return 0
except RuntimeError, e:
sys.stderr.write("Error: %s\n\n" % str(e))
if stage >= 0 and workDir is not None and os.path.isdir(workDir):
sys.stderr.write("Temporary data was left in: %s\n" % workDir)
if stage == 1:
sys.stderr.write("More information can be found in %s\n" %
os.path.join(workDir, "cactus.log"))
elif stage == 2:
sys.stderr.write("More information can be found in %s\n" %
os.path.join(workDir, "cactus.log"))
return -1