def runWorkflow_multipleExamples(inputGenFunction,
testNumber=1,
testRestrictions=(TestStatus.TEST_SHORT, TestStatus.TEST_MEDIUM, \
TestStatus.TEST_LONG, TestStatus.TEST_VERY_LONG,),
inverseTestRestrictions=False,
batchSystem="single_machine",
buildAvgs=False, buildReference=False,
buildReferenceSequence=False,
buildCactusPDF=False, buildAdjacencyPDF=False,
buildReferencePDF=False,
makeCactusTreeStats=False, makeMAFs=False,
configFile=None, buildJobTreeStats=False):
"""A wrapper to run a number of examples.
"""
if (inverseTestRestrictions and TestStatus.getTestStatus() not in testRestrictions) or \
(not inverseTestRestrictions and TestStatus.getTestStatus() in testRestrictions):
for test in xrange(testNumber):
tempDir = getTempDirectory(os.getcwd())
sequences, newickTreeString = inputGenFunction(regionNumber=test, tempDir=tempDir)
runWorkflow_TestScript(sequences, newickTreeString,
batchSystem=batchSystem,
buildAvgs=buildAvgs, buildReference=buildReference,
buildCactusPDF=buildCactusPDF, buildAdjacencyPDF=buildAdjacencyPDF,
makeCactusTreeStats=makeCactusTreeStats, makeMAFs=makeMAFs, configFile=configFile,
buildJobTreeStats=buildJobTreeStats)
system("rm -rf %s" % tempDir)
logger.info("Finished random test %i" % test)
def runWorkflow_multipleExamples(inputGenFunction,
testNumber=1,
testRestrictions=(TestStatus.TEST_SHORT, TestStatus.TEST_MEDIUM, \
TestStatus.TEST_LONG, TestStatus.TEST_VERY_LONG,),
inverseTestRestrictions=False,
batchSystem="single_machine",
buildAvgs=False, buildReference=False,
buildReferenceSequence=False,
buildCactusPDF=False, buildAdjacencyPDF=False,
buildReferencePDF=False,
makeCactusTreeStats=False, makeMAFs=False,
configFile=None, buildJobTreeStats=False):
"""A wrapper to run a number of examples.
"""
if (inverseTestRestrictions and TestStatus.getTestStatus() not in testRestrictions) or \
(not inverseTestRestrictions and TestStatus.getTestStatus() in testRestrictions):
for test in xrange(testNumber):
tempDir = getTempDirectory(os.getcwd())
sequences, newickTreeString = inputGenFunction(regionNumber=test,
tempDir=tempDir)
runWorkflow_TestScript(sequences,
newickTreeString,
batchSystem=batchSystem,
buildAvgs=buildAvgs,
buildReference=buildReference,
buildCactusPDF=buildCactusPDF,
buildAdjacencyPDF=buildAdjacencyPDF,
makeCactusTreeStats=makeCactusTreeStats,
makeMAFs=makeMAFs,
configFile=configFile,
buildJobTreeStats=buildJobTreeStats)
system("rm -rf %s" % tempDir)
logger.info("Finished random test %i" % test)
def runWorkflow_multipleExamples(inputGenFunction,
testNumber=1,
testRestrictions=(TestStatus.TEST_SHORT, TestStatus.TEST_MEDIUM, \
TestStatus.TEST_LONG, TestStatus.TEST_VERY_LONG,),
inverseTestRestrictions=False,
batchSystem="single_machine",
buildAvgs=False, buildReference=False,
configFile=None, buildToilStats=False,
useConstraints=False,
cactusWorkflowFunction=runCactusWorkflow,
buildHal=False,
buildFasta=False,
progressive=False):
"""A wrapper to run a number of examples.
"""
if (inverseTestRestrictions and TestStatus.getTestStatus() not in testRestrictions) or \
(not inverseTestRestrictions and TestStatus.getTestStatus() in testRestrictions):
for test in xrange(testNumber):
tempDir = getTempDirectory(os.getcwd())
if useConstraints:
sequences, newickTreeString, constraints = inputGenFunction(
regionNumber=test, tempDir=tempDir)
else:
sequences, newickTreeString = inputGenFunction(
regionNumber=test, tempDir=tempDir)
constraints = None
runWorkflow_TestScript(
sequences,
newickTreeString,
outputDir=tempDir,
batchSystem=batchSystem,
buildAvgs=buildAvgs,
buildReference=buildReference,
buildHal=buildHal,
buildFasta=buildFasta,
configFile=configFile,
buildToilStats=buildToilStats,
constraints=constraints,
progressive=progressive,
cactusWorkflowFunction=cactusWorkflowFunction)
system("rm -rf %s" % tempDir)
logger.info("Finished random test %i" % test)
def testSimulation(self):
if TestStatus.getTestStatus() == TestStatus.TEST_LONG:
blanchettePath = TestStatus.getPathToDataSets() + "/blanchettesSimulation/00.job"
outputPath = TestStatus.getPathToDataSets() + "/ortheus/blanchettesSimulationTest"
treeString = "(((((((((((((human:0.006969,chimp:0.009727):0.025291,((baboon:0.008968):0.011019):0.024581):0.023649):0.066673):0.018405,((rat:0.081244,mouse:0.072818):0.238435):0.021892):0.02326,(((cow:0.164728,(cat:0.109852,dog:0.107805):0.049576):0.004663):0.010883):0.033242):0.028346):0.016015):0.226853):0.063898):0.126639):0.119814):0.16696);"
seqFiles = ["HUMAN", "CHIMP", "BABOON", "RAT", "MOUSE", "COW", "CAT", "DOG"]
seqFiles = [blanchettePath + "/" + i for i in seqFiles]
outputFile = outputPath + "/outputJob1.mfa"
command = "Ortheus.py -e %s -d '%s' -f %s -j -a -b" % (" ".join(seqFiles), treeString, outputFile)
print "running command", command
system(command)
def runWorkflow_multipleExamples(inputGenFunction,
testNumber=1,
testRestrictions=(TestStatus.TEST_SHORT, TestStatus.TEST_MEDIUM, \
TestStatus.TEST_LONG, TestStatus.TEST_VERY_LONG,),
inverseTestRestrictions=False,
batchSystem="single_machine",
buildAvgs=False, buildReference=False,
configFile=None, buildJobTreeStats=False,
useConstraints=False,
cactusWorkflowFunction=runCactusWorkflow,
buildHal=False,
buildFasta=False,
progressive=False):
"""A wrapper to run a number of examples.
"""
if (inverseTestRestrictions and TestStatus.getTestStatus() not in testRestrictions) or \
(not inverseTestRestrictions and TestStatus.getTestStatus() in testRestrictions):
for test in xrange(testNumber):
tempDir = getTempDirectory(os.getcwd())
if useConstraints:
sequences, newickTreeString, constraints = inputGenFunction(regionNumber=test, tempDir=tempDir)
else:
sequences, newickTreeString = inputGenFunction(regionNumber=test, tempDir=tempDir)
constraints = None
experiment = runWorkflow_TestScript(sequences, newickTreeString,
outputDir=tempDir,
batchSystem=batchSystem,
buildAvgs=buildAvgs, buildReference=buildReference,
buildHal=buildHal,
buildFasta=buildFasta,
configFile=configFile,
buildJobTreeStats=buildJobTreeStats,
constraints=constraints,
progressive=progressive,
cactusWorkflowFunction=cactusWorkflowFunction)
experiment.cleanupDb()
system("rm -rf %s" % tempDir)
logger.info("Finished random test %i" % test)
def testAndyYatesFirstExample(self):
if TestStatus.getTestStatus() == TestStatus.TEST_LONG:
filePath = TestStatus.getPathToDataSets(
) + "/ortheus/andyYatesExample1"
seqs = "seq1.fa seq2.fa seq3.fa seq4.fa seq5.fa seq6.fa seq7.fa seq8.fa seq9.fa seq10.fa seq11.fa \
seq12.fa seq13.fa seq14.fa seq15.fa seq16.fa seq17.fa seq18.fa seq19.fa seq20.fa seq21.fa seq22.fa seq23.fa seq24.fa seq25.fa seq26.fa \
seq27.fa seq28.fa seq29.fa seq30.fa seq31.fa seq32.fa seq33.fa seq34.fa seq35.fa seq36.fa"
seqs = " ".join(["%s/%s" % (filePath, i) for i in seqs.split()])
command = 'Ortheus.py -l "#-j 0 -e" -e %s -z \
"(((1012:0.0112,1051:0.0119):0.0026,(1055:0.0015,1052:0.0018):0.0370):0.0022,1054:0.0108,1053:0.0116);" \
-A 1054 1051 1054 1054 1053 1012 1054 1054 1053 1054 1051 1054 1051 1051 1053 1051 1051 1012 1051 1054 1012 1054 1053 1051 1053 \
1054 1054 1051 1012 1012 1054 1053 1053 1012 1054 1051 -f %s/output.16163.mfa -g %s/output.16163.tree-a -k "# -A" -m "java -Xmx1800m -Xms1800m" -a -b' % \
(seqs, filePath, filePath)
print "running command", command
system(command)
def testSimulation(self):
if TestStatus.getTestStatus() == TestStatus.TEST_LONG:
blanchettePath = TestStatus.getPathToDataSets(
) + "/blanchettesSimulation/00.job"
outputPath = TestStatus.getPathToDataSets(
) + "/ortheus/blanchettesSimulationTest"
treeString = '(((((((((((((human:0.006969,chimp:0.009727):0.025291,((baboon:0.008968):0.011019):0.024581):0.023649):0.066673):0.018405,((rat:0.081244,mouse:0.072818):0.238435):0.021892):0.02326,(((cow:0.164728,(cat:0.109852,dog:0.107805):0.049576):0.004663):0.010883):0.033242):0.028346):0.016015):0.226853):0.063898):0.126639):0.119814):0.16696);'
seqFiles = [
"HUMAN", "CHIMP", "BABOON", "RAT", "MOUSE", "COW", "CAT", "DOG"
]
seqFiles = [blanchettePath + "/" + i for i in seqFiles]
outputFile = outputPath + "/outputJob1.mfa"
command = "Ortheus.py -e %s -d '%s' -f %s -j -a -b" % \
(" ".join(seqFiles), treeString, outputFile)
print "running command", command
system(command)
def testAndyYatesFirstExample(self):
if TestStatus.getTestStatus() == TestStatus.TEST_LONG:
filePath = TestStatus.getPathToDataSets() + "/ortheus/andyYatesExample1"
seqs = "seq1.fa seq2.fa seq3.fa seq4.fa seq5.fa seq6.fa seq7.fa seq8.fa seq9.fa seq10.fa seq11.fa \
seq12.fa seq13.fa seq14.fa seq15.fa seq16.fa seq17.fa seq18.fa seq19.fa seq20.fa seq21.fa seq22.fa seq23.fa seq24.fa seq25.fa seq26.fa \
seq27.fa seq28.fa seq29.fa seq30.fa seq31.fa seq32.fa seq33.fa seq34.fa seq35.fa seq36.fa"
seqs = " ".join(["%s/%s" % (filePath, i) for i in seqs.split()])
command = (
'Ortheus.py -l "#-j 0 -e" -e %s -z \
"(((1012:0.0112,1051:0.0119):0.0026,(1055:0.0015,1052:0.0018):0.0370):0.0022,1054:0.0108,1053:0.0116);" \
-A 1054 1051 1054 1054 1053 1012 1054 1054 1053 1054 1051 1054 1051 1051 1053 1051 1051 1012 1051 1054 1012 1054 1053 1051 1053 \
1054 1054 1051 1012 1012 1054 1053 1053 1012 1054 1051 -f %s/output.16163.mfa -g %s/output.16163.tree-a -k "# -A" -m "java -Xmx1800m -Xms1800m" -a -b'
% (seqs, filePath, filePath)
)
print "running command", command
system(command)
def testENm001(self):
if TestStatus.getTestStatus() == TestStatus.TEST_VERY_LONG:
encodePath = TestStatus.getPathToDataSets() + "/MAY-2005/ENm001"
outputPath = TestStatus.getPathToDataSets() + "/ortheus/encodeTest"
#treeString = '(((((((((((((human:0.006969,chimp:0.009727):0.025291,((baboon:0.008968):0.011019):0.024581):0.023649):0.066673):0.018405,((rat:0.081244,mouse:0.072818):0.238435):0.021892):0.02326,(((cow:0.164728,(cat:0.109852,dog:0.107805):0.049576):0.004663):0.010883):0.033242):0.028346):0.016015):0.226853):0.063898):0.126639):0.119814):0.16696);'
treeString = '((((human:0.006969,chimp:0.009727):0.025291,baboon:0.044568):0.108727,(rat:0.081244,mouse:0.072818):0.260327):0.02326,(cow:0.164728,(cat:0.109852,dog:0.107805):0.049576):0.048788):0.749525;'
seqFiles = [
"human.ENm001.fa", "chimp.ENm001.fa", "baboon.ENm001.fa",
"rat.ENm001.fa", "mouse.ENm001.fa", "cow.ENm001.fa",
"cat.ENm001.fa", "dog.ENm001.fa"
]
seqFiles = [encodePath + "/" + i for i in seqFiles]
outputFile = outputPath + "/outputENm001.mfa"
command = "Ortheus.py -e %s -d '%s' -f %s -j -a -b" % \
(" ".join(seqFiles), treeString, outputFile)
print "running command", command
system(command)
def testENm001(self):
if TestStatus.getTestStatus() == TestStatus.TEST_VERY_LONG:
encodePath = TestStatus.getPathToDataSets() + "/MAY-2005/ENm001"
outputPath = TestStatus.getPathToDataSets() + "/ortheus/encodeTest"
# treeString = '(((((((((((((human:0.006969,chimp:0.009727):0.025291,((baboon:0.008968):0.011019):0.024581):0.023649):0.066673):0.018405,((rat:0.081244,mouse:0.072818):0.238435):0.021892):0.02326,(((cow:0.164728,(cat:0.109852,dog:0.107805):0.049576):0.004663):0.010883):0.033242):0.028346):0.016015):0.226853):0.063898):0.126639):0.119814):0.16696);'
treeString = "((((human:0.006969,chimp:0.009727):0.025291,baboon:0.044568):0.108727,(rat:0.081244,mouse:0.072818):0.260327):0.02326,(cow:0.164728,(cat:0.109852,dog:0.107805):0.049576):0.048788):0.749525;"
seqFiles = [
"human.ENm001.fa",
"chimp.ENm001.fa",
"baboon.ENm001.fa",
"rat.ENm001.fa",
"mouse.ENm001.fa",
"cow.ENm001.fa",
"cat.ENm001.fa",
"dog.ENm001.fa",
]
seqFiles = [encodePath + "/" + i for i in seqFiles]
outputFile = outputPath + "/outputENm001.mfa"
command = "Ortheus.py -e %s -d '%s' -f %s -j -a -b" % (" ".join(seqFiles), treeString, outputFile)
print "running command", command
system(command)
