def progressiveFunction(self, experimentFile, toilDir,
batchSystem, buildAvgs,
buildReference,
buildHal,
buildFasta,
toilStats,
subtreeRoot=None):
tempDir = getTempDirectory(os.getcwd())
tempExperimentDir = os.path.join(tempDir, "exp")
runCreateMultiCactusProject(experimentFile,
tempExperimentDir,
fixNames=False,
root=subtreeRoot)
logger.info("Put the temporary files in %s" % tempExperimentDir)
runCactusProgressive(os.path.join(tempExperimentDir, "exp_project.xml"),
toilDir,
batchSystem=batchSystem,
buildAvgs=buildAvgs,
toilStats=toilStats)
# Check that the headers and sequences in the output are the
# same as the sequences in the input (minus differences in
# repeat-masking)
exp = ExperimentWrapper(ET.parse(experimentFile).getroot())
seqMap = exp.buildSequenceMap()
# Maps genome name -> headers in fasta
headers = {}
for genomeName, inputSequencePath in seqMap.items():
if os.path.isdir(inputSequencePath):
# Some "input sequence paths" are actually provided as
# directories containing multiple FASTAs
concatenatedPath = getTempFile()
system("cat %s/* > %s" % (inputSequencePath, concatenatedPath))
inputSequencePath = concatenatedPath
headers[genomeName] = list(map(itemgetter(0), fastaRead(inputSequencePath)))
# check headers inside .c2h output
for expPath in glob.glob('%s/*/*_experiment.xml' % (tempExperimentDir)):
subExp = ExperimentWrapper(ET.parse(expPath).getroot())
outgroups = subExp.getOutgroupEvents()
c2hPath = subExp.getHALPath()
with open(c2hPath) as f:
for line in f:
fields = line.split('\t')
if fields[0] == 's':
# Sequence line
genome = fields[1][1:-1]
header = fields[2][1:-1]
if genome in headers and genome not in outgroups:
# This genome is an input genome
self.assertTrue(header in headers[genome],
'Header %s from output c2h %s not found in input fa %s'
' for genome %s' % (header, c2hPath, seqMap[genome], genome))
runToilStatusAndFailIfNotComplete(toilDir)
system("rm -rf %s" % tempDir)
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,
outgroupNames=outgroups,
root=self.options.root)
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 progressiveFunction(self,
experimentFile,
toilDir,
batchSystem,
buildAvgs,
buildReference,
buildHal,
buildFasta,
toilStats,
subtreeRoot=None):
tempDir = getTempDirectory(os.getcwd())
tempExperimentDir = os.path.join(tempDir, "exp")
runCreateMultiCactusProject(experimentFile,
tempExperimentDir,
fixNames=False,
root=subtreeRoot)
logger.info("Put the temporary files in %s" % tempExperimentDir)
runCactusProgressive(os.path.join(tempExperimentDir,
"exp_project.xml"),
toilDir,
batchSystem=batchSystem,
buildAvgs=buildAvgs,
toilStats=toilStats)
# Check that the headers and sequences in the output are the
# same as the sequences in the input (minus differences in
# repeat-masking)
exp = ExperimentWrapper(ET.parse(experimentFile).getroot())
seqMap = exp.buildSequenceMap()
# Maps genome name -> headers in fasta
headers = {}
for genomeName, inputSequencePath in seqMap.items():
if os.path.isdir(inputSequencePath):
# Some "input sequence paths" are actually provided as
# directories containing multiple FASTAs
concatenatedPath = getTempFile()
system("cat %s/* > %s" % (inputSequencePath, concatenatedPath))
inputSequencePath = concatenatedPath
headers[genomeName] = list(
map(itemgetter(0), fastaRead(inputSequencePath)))
# check headers inside .c2h output
for expPath in glob.glob('%s/*/*_experiment.xml' %
(tempExperimentDir)):
subExp = ExperimentWrapper(ET.parse(expPath).getroot())
outgroups = subExp.getOutgroupEvents()
c2hPath = subExp.getHALPath()
with open(c2hPath) as f:
for line in f:
fields = line.split('\t')
if fields[0] == 's':
# Sequence line
genome = fields[1][1:-1]
header = fields[2][1:-1]
if genome in headers and genome not in outgroups:
# This genome is an input genome
self.assertTrue(
header in headers[genome],
'Header %s from output c2h %s not found in input fa %s'
' for genome %s' %
(header, c2hPath, seqMap[genome], genome))
runToilStatusAndFailIfNotComplete(toilDir)
system("rm -rf %s" % tempDir)