def runCactusAddReferenceCoordinates(cactusDiskDatabaseString, flowerNames, logLevel=None, referenceEventString=None, outgroupEventString=None, secondaryDatabaseString=None, bottomUpPhase=None):
logLevel = getLogLevelString2(logLevel)
bottomUpPhase = nameValue("bottomUpPhase", bottomUpPhase, bool)
referenceEventString = nameValue("referenceEventString", referenceEventString)
outgroupEventString = nameValue("outgroupEventString", outgroupEventString)
secondaryDatabaseString = nameValue("secondaryDisk", secondaryDatabaseString, quotes=True)
command = "cactus_addReferenceCoordinates --cactusDisk '%s' %s --logLevel %s %s %s %s" % (cactusDiskDatabaseString, secondaryDatabaseString, logLevel, referenceEventString, outgroupEventString, bottomUpPhase)
popenPush(command, stdinString=flowerNames)
def runCactusPhylogeny(cactusDiskDatabaseString,
flowerNames=encodeFlowerNames((0,)),
logLevel=None):
logLevel = getLogLevelString2(logLevel)
command = "cactus_phylogeny --cactusDisk '%s' --logLevel %s" % \
(cactusDiskDatabaseString, logLevel)
popenPush(command, stdinString=flowerNames)
logger.info("Ran cactus_phylogeny okay")
def runCactusCheck(cactusDiskDatabaseString,
flowerNames=encodeFlowerNames((0,)),
logLevel=None,
recursive=None,
checkNormalised=None):
logLevel = getLogLevelString2(logLevel)
recursive = nameValue("recursive", recursive, bool)
checkNormalised = nameValue("checkNormalised", checkNormalised, bool)
popenPush("cactus_check --cactusDisk '%s' --logLevel %s %s %s" % (cactusDiskDatabaseString, logLevel, recursive, checkNormalised), stdinString=flowerNames)
logger.info("Ran cactus check")
def run(self):
cmdline = self.prepOptions.cmdLine.replace("IN_FILE", '"' + self.inChunk + '"')
cmdline = cmdline.replace("OUT_FILE", '"' + self.outChunk + '"')
cmdline = cmdline.replace("TEMP_DIR", '"' + self.getLocalTempDir() + '"')
cmdline = cmdline.replace("PROPORTION_SAMPLED", str(self.proportionSampled))
logger.info("Preprocessor exec " + cmdline)
# print "command", cmdline
# sys.exit(1)
popenPush(cmdline, " ".join(self.seqPaths))
if self.prepOptions.check:
system("cp %s %s" % (self.inChunk, self.outChunk))
def runCactusHalGenerator(cactusDiskDatabaseString,
secondaryDatabaseString,
flowerNames,
referenceEventString,
outputFile=None,
showOnlySubstitutionsWithRespectToReference=None,
logLevel=None):
logLevel = getLogLevelString2(logLevel)
popenPush("cactus_halGenerator --cactusDisk '%s' --secondaryDisk '%s' --logLevel %s %s %s %s" %
(cactusDiskDatabaseString, secondaryDatabaseString, logLevel,
nameValue("referenceEventString", referenceEventString),
nameValue("outputFile", outputFile),
nameValue("showOnlySubstitutionsWithRespectToReference",
showOnlySubstitutionsWithRespectToReference, bool)),
stdinString=flowerNames)
def runCactusMakeNormal(cactusDiskDatabaseString, flowerNames, maxNumberOfChains=0, logLevel=None):
"""Makes the given flowers normal (see normalisation for the various phases)
"""
logLevel = getLogLevelString2(logLevel)
popenPush("cactus_normalisation --cactusDisk '%s' --maxNumberOfChains %i --logLevel %s" % (cactusDiskDatabaseString, maxNumberOfChains, logLevel), stdinString=flowerNames)
def runCactusAdjacencies(cactusDiskDatabaseString, flowerNames=encodeFlowerNames((0,)), logLevel=None):
logLevel = getLogLevelString2(logLevel)
command = "cactus_fillAdjacencies --cactusDisk '%s' --logLevel %s" %\
(cactusDiskDatabaseString, logLevel)
popenPush(command, stdinString=flowerNames)
logger.info("Ran cactus_fillAdjacencies OK")
def run(self):
popenPush("cactus_batch_mergeChunks > %s" % self.outSequencePath, " ".join(self.chunkList))
