def testMCSAlignAtomMap(self):
"""Test case - match test with return of atom maps"""
self.__lfh.write("\nStarting OeAlignDepictTests testMCSAlignAtomMap\n")
try:
pairIdList = self.__readPairList(fn=self.__rnaPairFile)
oed = OeDepictMCSAlign(verbose=self.__verbose, log=self.__lfh)
for refId, fitId in pairIdList:
oed.setRefId(refId, cachePath=self.__topCachePath)
oed.setFitId(fitId, cachePath=self.__topCachePath)
aML = oed.testAlign()
if len(aML) > 0:
self.__lfh.write("Match suceeded for: %s %s\n" %
(refId, fitId))
else:
self.__lfh.write("Match failed for: %s %s\n" %
(refId, fitId))
except: # noqa: E722 pylint: disable=bare-except
traceback.print_exc(file=self.__lfh)
self.fail()
def testMCSAlignListDepict(self):
"""Test case - List view of pairwise MCS alignment - multipage output"""
self.__lfh.write(
"\nStarting OeAlignDepictTests testMCSAlignListDepict\n")
try:
oed = OeDepictMCSAlign(verbose=self.__verbose, log=self.__lfh)
oed.setRefId(self.__refId, cachePath=self.__topCachePath)
oed.setFitIdList(self.__idList, cachePath=self.__topCachePath)
imageFile = os.path.join(self.__testoutput,
"list-example-mcs-alignment.pdf")
aML = oed.alignPairList(imagePath=imageFile)
if len(aML) > 0:
for (rCC, rAt, tCC, tAt) in aML:
self.__lfh.write("%5s %-5s %5s %-5s\n" %
(rCC, rAt, tCC, tAt))
except: # noqa: E722 pylint: disable=bare-except
traceback.print_exc(file=self.__lfh)
self.fail()
def testMCSAlignPairDepict(self):
"""Test case - Simple pairwise MCSS alignment - Each aligned pair output to a separate image file"""
self.__lfh.write(
"\nStarting OeAlignDepictTests tstMCSalignPairDepict\n")
try:
oed = OeDepictMCSAlign(verbose=self.__verbose, log=self.__lfh)
oed.setRefId(self.__refId, cachePath=self.__topCachePath)
for fitId in self.__idList:
oed.setFitId(fitId, cachePath=self.__topCachePath)
fName = os.path.join(
self.__testoutput,
"ref-" + self.__refId + "-trg-" + fitId + ".png")
aML = oed.alignPair(imagePath=fName)
if len(aML) > 0:
for (rCC, rAt, tCC, tAt) in aML:
self.__lfh.write("%5s %-5s %5s %-5s\n" %
(rCC, rAt, tCC, tAt))
except: # noqa: E722 pylint: disable=bare-except
traceback.print_exc(file=self.__lfh)
self.fail()