def cactusPrepare(options, project):
""" annotate a SeqFile with ancestral names as well as paths for output sequences."""
# read the input
seqFile = SeqFile(options.seqFile)
configNode = ET.parse(options.configFile).getroot()
config = ConfigWrapper(configNode)
# prepare output sequence directory
# todo: support remote (ie s3) output directory
try:
os.makedirs(options.outSeqDir)
except:
pass
if not os.path.isdir(options.outSeqDir):
raise RuntimeError('Unable to create output sequence directory \'{}\''.format(options.outSeqDir))
if not os.access(options.outSeqDir, os.W_OK):
logger.warning('Output sequence directory is not writeable: \'{}\''.format(options.outSeqDir))
# hack the configfile to skip preprocessing and write it to the output dir
if options.preprocessOnly:
config.removePreprocessors()
options.configFile = os.path.join(options.outSeqDir, 'config.xml')
config.writeXML(options.configFile)
# pass through the config file to the options
# todo (don't like second hard-code check of .xml path)
if options.configFile != os.path.join(cactusRootPath(), "cactus_progressive_config.xml"):
options.cactusOptions += ' --configFile {}'.format(options.configFile)
# get the ancestor names
tree = MultiCactusTree(seqFile.tree)
tree.nameUnlabeledInternalNodes(prefix = config.getDefaultInternalNodePrefix())
# make the output
outSeqFile = SeqFile()
outSeqFile.tree= tree
outSeqFile.pathMap = seqFile.pathMap
outSeqFile.outgroups = seqFile.outgroups
# update paths for preprocessed leaves or inferred ancestors
for node in outSeqFile.tree.breadthFirstTraversal():
name = outSeqFile.tree.getName(node)
leaf = outSeqFile.tree.isLeaf(node)
if leaf or (not leaf and name not in seqFile.pathMap and not options.preprocessOnly):
out_basename = seqFile.pathMap[name] if name in seqFile.pathMap else '{}.fa'.format(name)
outSeqFile.pathMap[name] = os.path.join(options.outSeqDir, os.path.basename(out_basename))
# write the output
with open(options.outSeqFile, 'w') as out_sf:
out_sf.write(str(outSeqFile))
# write the instructions
print(get_plan(options, project, outSeqFile))
def cactusPrepare(options, project):
""" annotate a SeqFile with ancestral names as well as paths for output sequences."""
# read the input
seqFile = SeqFile(options.seqFile)
configNode = ET.parse(options.configFile).getroot()
config = ConfigWrapper(configNode)
if not options.wdl:
# prepare output sequence directory
# todo: support remote (ie s3) output directory
try:
os.makedirs(options.outDir)
except:
pass
if not os.path.isdir(options.outDir):
raise RuntimeError('Unable to create output sequence directory \'{}\''.format(options.outDir))
if not os.access(options.outDir, os.W_OK):
logger.warning('Output sequence directory is not writeable: \'{}\''.format(options.outDir))
if options.preprocessOnly or options.gpu:
if options.preprocessOnly:
# hack the configfile to skip preprocessing and write it to the output dir
config.removePreprocessors()
if options.gpu:
# hack the configfile to toggle on gpu lastz
cafNode = findRequiredNode(config.xmlRoot, "caf")
cafNode.attrib["gpuLastz"] = "true"
# realigning doesn't mix well with lastz so we make sure it's off
# https://github.com/ComparativeGenomicsToolkit/cactus/issues/271
cafNode.attrib["realign"] = "0"
options.configFile = os.path.join(options.outDir, 'config-prepared.xml')
sys.stderr.write("configuration saved in {}\n".format(options.configFile))
config.writeXML(options.configFile)
# pass through the config file to the options
# todo (don't like second hard-code check of .xml path)
if options.configFile != os.path.join(cactusRootPath(), "cactus_progressive_config.xml") and not options.wdl:
options.cactusOptions += ' --configFile {}'.format(options.configFile)
# get the ancestor names
tree = MultiCactusTree(seqFile.tree)
tree.nameUnlabeledInternalNodes(prefix = config.getDefaultInternalNodePrefix())
# make the output
outSeqFile = SeqFile()
outSeqFile.tree= tree
outSeqFile.pathMap = copy.deepcopy(seqFile.pathMap)
outSeqFile.outgroups = copy.deepcopy(seqFile.outgroups)
# update paths for preprocessed leaves or inferred ancestors
for node in outSeqFile.tree.breadthFirstTraversal():
name = outSeqFile.tree.getName(node)
leaf = outSeqFile.tree.isLeaf(node)
if leaf or (not leaf and name not in seqFile.pathMap and not options.preprocessOnly):
out_basename = seqFile.pathMap[name] if name in seqFile.pathMap else '{}.fa'.format(name)
outSeqFile.pathMap[name] = os.path.join(options.outDir, os.path.basename(out_basename))
if options.wdl:
# uniquify name in wdl to prevent collisions
outSeqFile.pathMap[name] += '.pp'
# write the output
if options.outSeqFile:
with open(options.outSeqFile, 'w') as out_sf:
out_sf.write(str(outSeqFile))
# write the instructions
print(get_plan(options, project, seqFile, outSeqFile))