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cPecanRealignTest.py
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cPecanRealignTest.py
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import unittest
import os, sys
from sonLib.bioio import cigarReadFromString, cigarWrite
from sonLib.bioio import popenCatch
from sonLib.bioio import logger
from sonLib.bioio import TestStatus
from sonLib.bioio import getTempFile
from sonLib.bioio import system
from sonLib.bioio import parseSuiteTestOptions, getLogLevelString
class TestCase(unittest.TestCase):
def setUp(self):
unittest.TestCase.setUp(self)
def tearDown(self):
unittest.TestCase.tearDown(self)
def testCPecanRealignDummy(self):
"""Runs cPecanRealign using the "rescoreOriginalAlignment" mode
and checks the output is equivalent to what you'd get by just running lastz.
"""
for seqFile1, seqFile2 in seqFilePairGenerator():
realignCommand, lastzCommand = getCommands(seqFile1, seqFile2, "--rescoreOriginalAlignment")
for realignLine, lastzLine in zip([ i for i in popenCatch(realignCommand).split("\n") if i != '' ],
[ i for i in popenCatch(lastzCommand).split("\n") if i != '' ]):
realignCigar = cigarReadFromString(realignLine)
lastzCigar = cigarReadFromString(lastzLine)
self.assertTrue(realignCigar != None)
self.assertTrue(realignCigar == lastzCigar)
def testCPecanRealign(self):
"""Runs cPecanRealign using the default parameters and checks that the realigned output cigars align
the same subsequences.
"""
for seqFile1, seqFile2 in seqFilePairGenerator():
realignCommand, lastzCommand = getCommands(seqFile1, seqFile2)
for realignLine, lastzLine in zip([ i for i in popenCatch(realignCommand).split("\n") if i != '' ],
[ i for i in popenCatch(lastzCommand).split("\n") if i != '' ]):
realignCigar = cigarReadFromString(realignLine)
lastzCigar = cigarReadFromString(lastzLine)
self.assertTrue(realignCigar.sameCoordinates(lastzCigar))
def testCPecanRealignSplitSequences(self):
"""Runs cPecanRealign, splitting indels longer than 100bp, and check
that the coverage from the results is the same as the coverage from
realigning with no arguments.."""
for seqFile1, seqFile2 in seqFilePairGenerator():
# Drop the lastz command since it's not needed. But this
# is still convenient to use the same parameters as all
# the other tests
realignCommand, _ = getCommands(seqFile1, seqFile2)
splitRealignCommand = realignCommand + " --splitIndelsLongerThanThis 100"
realignOutput = getTempFile()
splitRealignOutput = getTempFile()
realignCommand += " > %s" % realignOutput
splitRealignCommand += " > %s" % splitRealignOutput
system(realignCommand)
system(splitRealignCommand)
# Check coverage on seqFile1
#The following will fail until we refactor.
splitRealignCoverage = popenCatch("cactus_coverage %s %s" % (seqFile1, splitRealignOutput))
realignCoverage = popenCatch("cactus_coverage %s %s" % (seqFile1, realignOutput))
self.assertTrue(splitRealignCoverage == realignCoverage)
# Check coverage on seqFile2
splitRealignCoverage = popenCatch("cactus_coverage %s %s" % (seqFile2, splitRealignOutput))
realignCoverage = popenCatch("cactus_coverage %s %s" % (seqFile2, realignOutput))
self.assertTrue(splitRealignCoverage == realignCoverage)
os.remove(realignOutput)
os.remove(splitRealignOutput)
def testCPecanRealignRescoreByIdentityAndProb(self):
"""Runs cactus realign using the default parameters and checks that the realigned output cigars align
the same subsequences.
"""
for seqFile1, seqFile2 in seqFilePairGenerator():
realignCommandByIdentity, lastzCommand = getCommands(seqFile1, seqFile2, realignArguments="--rescoreByIdentity")
realignCommandByPosteriorProb = getCommands(seqFile1, seqFile2, realignArguments="--rescoreByPosteriorProb")[0]
realignCommandByIdentityIgnoringGaps = getCommands(seqFile1, seqFile2, realignArguments="--rescoreByIdentityIgnoringGaps")[0]
for realignLineByIdentity, realignLineByPosteriorProb, realignLineByIdentityIgnoringGaps, lastzLine in \
zip([ i for i in popenCatch(realignCommandByIdentity).split("\n") if i != '' ], \
[ i for i in popenCatch(realignCommandByPosteriorProb).split("\n") if i != '' ], \
[ i for i in popenCatch(realignCommandByIdentityIgnoringGaps).split("\n") if i != '' ], \
[ i for i in popenCatch(lastzCommand).split("\n") if i != '' ]):
realignCigarByIdentity = cigarReadFromString(realignLineByIdentity)
realignCigarByPosteriorProb = cigarReadFromString(realignLineByPosteriorProb)
realignCigarByIdentityIgnoringGaps = cigarReadFromString(realignLineByIdentityIgnoringGaps)
lastzCigar = cigarReadFromString(lastzLine)
#Check scores are as expected
self.assertTrue(realignCigarByIdentity.score >= 0)
self.assertTrue(realignCigarByIdentity.score <= 100.0)
self.assertTrue(realignCigarByPosteriorProb.score >= 0)
self.assertTrue(realignCigarByPosteriorProb.score <= 100.0)
self.assertTrue(realignCigarByIdentityIgnoringGaps.score >= 0)
self.assertTrue(realignCigarByIdentityIgnoringGaps.score <= 100.0)
#print "Scores", "Rescore by identity", realignCigarByIdentity.score, "Rescore by posterior prob", realignCigarByPosteriorProb.score, "Rescore by identity ignoring gaps", realignCigarByIdentityIgnoringGaps.score, "Lastz score", lastzCigar.score
def getCommands(seqFile1, seqFile2, realignArguments="", lastzArguments="--ambiguous=iupac"):
lastzCommand = "cPecanLastz --format=cigar %s %s[multiple][nameparse=darkspace] %s[nameparse=darkspace]" % (lastzArguments, seqFile1, seqFile2)
realignCommand = "%s | cPecanRealign %s %s %s" % (lastzCommand, realignArguments, seqFile1, seqFile2)
return realignCommand, lastzCommand
def seqFilePairGenerator():
##Get sequences
encodePath = os.path.join(TestStatus.getPathToDataSets(), "MAY-2005")
encodeRegions = [ "ENm00" + str(i) for i in xrange(1,2) ] #, 2) ] #Could go to six
species = ("human", "mouse") #, "dog")#, "chimp")
#Other species to try "rat", "monodelphis", "macaque", "chimp"
for encodeRegion in encodeRegions:
regionPath = os.path.join(encodePath, encodeRegion)
for i in xrange(len(species)):
species1 = species[i]
for species2 in species[i+1:]:
seqFile1 = os.path.join(regionPath, "%s.%s.fa" % (species1, encodeRegion))
seqFile2 = os.path.join(regionPath, "%s.%s.fa" % (species2, encodeRegion))
yield seqFile1, seqFile2
def main():
parseSuiteTestOptions()
unittest.main()
if __name__ == '__main__':
main()