def doTestMapCds(self, contained):
destAlns = loadPslFile(self.getInputFile("clonesWeird.psl"),
inclUnaln=True)
srcAlns = loadPslFile(self.getInputFile("refseqWeird.psl"),
self.getInputFile("refseqWeird.cds"),
inclUnaln=True,
projectCds=True)
mappedAlns = []
for destAln in destAlns:
for srcAln in srcAlns:
if srcAln.qSeq.cds == None:
raise Exception("no qCDS: " + srcAln.qSeq.id + " <=> " + srcAln.tSeq.id)
if srcAln.tSeq.cds == None:
raise Exception("no tCDS: " + srcAln.qSeq.id + " <=> " + srcAln.tSeq.id)
if srcAln.targetOverlap(destAln):
ma = destAln.copy()
ma.mapCds(srcAln, srcAln.tSeq, ma.tSeq, contained=contained)
mappedAlns.append(WithSrcCds(srcAln, ma))
self.__dumpNDiff(mappedAlns, ".out")
def testRevCmpl(self):
alns = loadPslFile(self.getInputFile("hsRefSeq.psl"),
self.getInputFile("hsRefSeq.cds"))
ralns = []
rralns = []
for pa in alns:
rpa = pa.revCmpl()
ralns.append(rpa)
rralns.append(rpa.revCmpl())
self.__dumpNDiff(ralns, ".rout")
self.__dumpNDiff(rralns, ".rrout")
def testRevCmpl(self):
alns = loadPslFile(self.getInputFile("hsRefSeq.psl"),
self.getInputFile("hsRefSeq.cds"))
ralns = []
rralns = []
for pa in alns:
rpa = pa.revCmpl()
ralns.append(rpa)
rralns.append(rpa.revCmpl())
self.__dumpNDiff(ralns, ".rout")
self.__dumpNDiff(rralns, ".rrout")
def doTestProjectCds(self, contained):
alns = loadPslFile(self.getInputFile("refseqWeird.psl"),
self.getInputFile("refseqWeird.cds"),
inclUnaln=True)
qalns = []
for pa in alns:
pa.projectCdsToTarget(contained=contained)
# project back
qpa = pa.copy()
qpa.qSubSeqs.clearCds()
qpa.projectCdsToQuery(contained=contained)
qalns.append(qpa)
self.__dumpNDiff(alns, ".tout")
self.__dumpNDiff(qalns, ".qout")
def doTestProjectCds(self, contained):
alns = loadPslFile(self.getInputFile("refseqWeird.psl"),
self.getInputFile("refseqWeird.cds"),
inclUnaln=True)
qalns = []
for pa in alns:
pa.projectCdsToTarget(contained=contained)
# project back
qpa = pa.copy()
qpa.qSubSeqs.clearCds()
qpa.projectCdsToQuery(contained=contained)
qalns.append(qpa)
self.__dumpNDiff(alns, ".tout")
self.__dumpNDiff(qalns, ".qout")
def doTestMapCds(self, contained):
destAlns = loadPslFile(self.getInputFile("clonesWeird.psl"),
inclUnaln=True)
srcAlns = loadPslFile(self.getInputFile("refseqWeird.psl"),
self.getInputFile("refseqWeird.cds"),
inclUnaln=True,
projectCds=True)
mappedAlns = []
for destAln in destAlns:
for srcAln in srcAlns:
if srcAln.qSeq.cds == None:
raise Exception("no qCDS: " + srcAln.qSeq.id + " <=> " +
srcAln.tSeq.id)
if srcAln.tSeq.cds == None:
raise Exception("no tCDS: " + srcAln.qSeq.id + " <=> " +
srcAln.tSeq.id)
if srcAln.targetOverlap(destAln):
ma = destAln.copy()
ma.mapCds(srcAln,
srcAln.tSeq,
ma.tSeq,
contained=contained)
mappedAlns.append(WithSrcCds(srcAln, ma))
self.__dumpNDiff(mappedAlns, ".out")
def testLoadUnaln(self):
alns = loadPslFile(self.getInputFile("hsRefSeq.psl"),
self.getInputFile("hsRefSeq.cds"),
inclUnaln=True)
self.__dumpNDiff(alns, ".out")
def testLoad(self):
alns = loadPslFile(self.getInputFile("hsRefSeq.psl"),
self.getInputFile("hsRefSeq.cds"))
self.__dumpNDiff(alns, ".out")
def testLoadUnaln(self):
alns = loadPslFile(self.getInputFile("hsRefSeq.psl"),
self.getInputFile("hsRefSeq.cds"),
inclUnaln=True)
self.__dumpNDiff(alns, ".out")
def testLoad(self):
alns = loadPslFile(self.getInputFile("hsRefSeq.psl"),
self.getInputFile("hsRefSeq.cds"))
self.__dumpNDiff(alns, ".out")