def testRandom(self):
"""Makes random sequences and tests that Ortheus can align them and produce a valid output.
"""
outputFile = getTempFile()
self.tempFiles.append(outputFile)
MAX_SEQS = 20
for i in xrange(MAX_SEQS):
self.tempFiles.append(getTempFile())
for test in xrange(0, self.testNo):
print "test no : %i " % test
#seqNo
binaryTree = randomTree()
middleSeq = getRandomSequence(250)[1]
seqs = []
getTreeSeqs(binaryTree, middleSeq, seqs)
if len(seqs) <= MAX_SEQS and len(seqs) > 2:
seqFiles = []
for i in xrange(0, len(seqs)):
seqFiles.append(self.tempFiles[1 + i])
fileHandle = open(seqFiles[i], 'w')
fastaWrite(fileHandle, "%i" % i, seqs[i])
fileHandle.close()
print "Have seq files ", seqFiles
treeString = printBinaryTree(binaryTree, True)
print "For tree ", treeString
#align seqs and check no failure
command = "ortheus_core -a %s -b '%s' -d %s -e" % (
" ".join(seqFiles), treeString, outputFile)
print "command to call", command
system(command)
#check alignment is complete
alignment = [i[:] for i in fastaAlignmentRead(outputFile)]
#print "alignment", alignment
checkAlignment(alignment, seqs)
print "test no is finished : %i " % test
def testRandom(self):
"""Makes random sequences and tests that Ortheus can align them and produce a valid output.
"""
outputFile = getTempFile()
self.tempFiles.append(outputFile)
MAX_SEQS = 20
for i in xrange(MAX_SEQS):
self.tempFiles.append(getTempFile())
for test in xrange(0, self.testNo):
print "test no : %i " % test
# seqNo
binaryTree = randomTree()
middleSeq = getRandomSequence(250)[1]
seqs = []
getTreeSeqs(binaryTree, middleSeq, seqs)
if len(seqs) <= MAX_SEQS and len(seqs) > 2:
seqFiles = []
for i in xrange(0, len(seqs)):
seqFiles.append(self.tempFiles[1 + i])
fileHandle = open(seqFiles[i], "w")
fastaWrite(fileHandle, "%i" % i, seqs[i])
fileHandle.close()
print "Have seq files ", seqFiles
treeString = printBinaryTree(binaryTree, True)
print "For tree ", treeString
# align seqs and check no failure
command = "ortheus_core -a %s -b '%s' -d %s -e" % (" ".join(seqFiles), treeString, outputFile)
print "command to call", command
system(command)
# check alignment is complete
alignment = [i[:] for i in fastaAlignmentRead(outputFile)]
# print "alignment", alignment
checkAlignment(alignment, seqs)
print "test no is finished : %i " % test
def testCactusWorkflow_Blanchette(self):
"""Runs the workflow on blanchette's simulated (colinear) regions.
"""
if "SON_TRACE_DATASETS" not in os.environ:
return
for test in xrange(self.testNo):
tempFiles = []
tempDir = getTempDirectory(os.getcwd())
trueAlignment = os.path.join(TestStatus.getPathToDataSets(), "blanchettesSimulation", "00.job", "true.mfa")
#Load the true alignment.
columnAlignment = [ i for i in fastaAlignmentRead(trueAlignment) ]
fastaHeaders = [ i for i in fastaReadHeaders(trueAlignment) ]
sequenceNumber = 9
#The tree
newickTreeString = "((((HUMAN:0.006969, CHIMP:0.009727):0.025291, BABOON:0.044568):0.11,(RAT:0.072818, MOUSE:0.081244):0.260342):0.023260,((DOG:0.07, CAT:0.07):0.087381,(PIG:0.06, COW:0.06):0.104728):0.04);"
#Get random dir
testDir = getTempDirectory(tempDir)
#random alignment
alignmentLength = 5000
randomStart = random.choice(xrange(len(columnAlignment)-alignmentLength))
subAlignment = columnAlignment[randomStart:randomStart+alignmentLength]
logger.info("Got a sub alignment, it is %i columns long" % len(subAlignment))
#Get sequences
sequences = [ (fastaHeaders[seqNo], "".join([ column[seqNo] for column in subAlignment if column[seqNo] != '-' ])) for seqNo in xrange(sequenceNumber) ]
logger.info("Got the sequences")
#Write sequences into temp files
tempFastaFiles = []
for seqNo in xrange(sequenceNumber):
header, sequence = sequences[seqNo]
logger.info("Making temp file for header: %s, seq: %s" % (header, sequence))
tempFastaFile = os.path.join(testDir, "%i.fa" % seqNo)
tempFastaFiles.append(tempFastaFile)
fileHandle = open(tempFastaFile, "w")
fastaWrite(fileHandle, header, sequence)
fileHandle.close()
logger.info("Got the temp sequence files")
experiment = getCactusWorkflowExperimentForTest(tempFastaFiles, newickTreeString, testDir)
experimentFile = os.path.join(testDir, "experiment.xml")
experiment.writeXML(experimentFile)
cactusDiskDatabaseString = experiment.getDiskDatabaseString()
jobTree = os.path.join(testDir, "jobTree")
runCactusWorkflow(experimentFile, jobTree)
logger.info("Ran the the workflow")
#Check the output alignment
runJobTreeStatusAndFailIfNotComplete(jobTree)
logger.info("Checked the job tree dir")
#Output the 'TRUE' alignment file
if os.system("mfaToMaf --help > /dev/null 2>&1") == 0 and\
os.system("cactus_MAFGenerator --help > /dev/null 2>&1") == 0 and\
os.system("mafComparator --help > /dev/null 2>&1") == 0 and\
os.system("cactus_treeStats --help > /dev/null 2>&1") == 0:
trueMFAFile = os.path.join(testDir, "true.mfa")
fastaAlignmentWrite(subAlignment, fastaHeaders, len(fastaHeaders), trueMFAFile)
trueMAFFile = os.path.join(testDir, "true.maf")
system("mfaToMaf --mfaFile %s --outputFile %s --logLevel %s" % (trueMFAFile, trueMAFFile, getLogLevelString()))
system("cat %s" % trueMAFFile)
#Now get mafs for the region.
mAFFile = os.path.join(testDir, "flower.maf")
system("cactus_MAFGenerator --flowerName 0 --cactusDisk '%s' --outputFile %s --logLevel %s" % (cactusDiskDatabaseString, mAFFile, getLogLevelString()))
logger.info("Got the MAFs from the flower disk")
system("cat %s" % mAFFile)
statsFile = os.path.join(testDir, "stats.xml")
system("cactus_treeStats --cactusDisk '%s' --flowerName 0 --outputFile %s --logLevel %s" % (cactusDiskDatabaseString, statsFile, getLogLevelString()))
system("cat %s" % statsFile)
logger.info("Got the cactus tree stats")
#Now compare the mafs to the output.
resultsFile = os.path.join(testDir, "results.xml")
system("mafComparator --mafFile1 %s --mafFile2 %s --outputFile %s --logLevel %s" % (trueMAFFile, mAFFile, resultsFile, getLogLevelString()))
logger.info("Ran the maf comparator")
system("cat %s" % resultsFile)
#Cleanup
experiment.cleanupDb()
system("rm -rf %s" % testDir)
logger.info("Successfully ran test for the problem")
for tempFile in tempFiles:
os.remove(tempFile)
system("rm -rf %s" % tempDir)