def test_gmapCreateDB_case1(self):
"""Test _gmapCreateDB(refFile, isWithinRepository, tempRootDir).
Condition: the reference is not within a reference repository.
"""
# Case 1: the reference is not within a reference repository
files = PBAlignFiles()
parser = argparse.ArgumentParser()
argumentList = [self.queryFofn, self.refFa, self.outSam,
'--algorithm', 'gmap']
parser, options, _info = parseOptions(argumentList=argumentList,
parser=parser)
service = GMAPService(options, files)
dbRoot, dbName = service._gmapCreateDB(self.refFa, False, self.outDir)
self.assertTrue(path.exists(dbRoot))
self.assertTrue(path.exists(path.join(dbRoot, dbName)))
def test_gmapCreateDB_case1(self):
"""Test _gmapCreateDB(refFile, isWithinRepository, tempRootDir).
Condition: the reference is not within a reference repository.
"""
# Case 1: the reference is not within a reference repository
files = PBAlignFiles()
parser = argparse.ArgumentParser()
argumentList = [
self.queryFofn, self.refFa, self.outSam, '--algorithm', 'gmap'
]
parser, options, _info = parseOptions(argumentList=argumentList,
parser=parser)
service = GMAPService(options, files)
dbRoot, dbName = service._gmapCreateDB(self.refFa, False, self.outDir)
self.assertTrue(path.exists(dbRoot))
self.assertTrue(path.exists(path.join(dbRoot, dbName)))
def _createAlignService(self, name, args, fileNames, tempFileManager):
"""
Create and return an AlignService by algorithm name.
Input:
name : an algorithm name such as blasr
fileNames : an PBAlignFiles object
args : pbalign options
tempFileManager: a temporary file manager
Output:
an object of AlignService subclass (such as BlasrService).
"""
if name not in ALGORITHM_CANDIDATES:
errMsg = "ERROR: unrecognized algorithm {algo}".format(algo=name)
logging.error(errMsg)
raise ValueError(errMsg)
service = None
if name == "blasr":
service = BlasrService(args, fileNames, tempFileManager)
elif name == "bowtie":
service = BowtieService(args, fileNames, tempFileManager)
elif name == "gmap":
service = GMAPService(args, fileNames, tempFileManager)
else:
errMsg = "Service for {algo} is not implemented.".\
format(algo=name)
logging.error(errMsg)
raise ValueError(errMsg)
service.checkAvailability()
return service
def test_gmapCreateDB_case2(self):
"""Test _gmapCreateDB(refFile, isWithinRepository, tempRootDir).
Condition: the reference is within a reference repository.
"""
# Case 2: the reference is within a reference repository
files = PBAlignFiles()
parser = argparse.ArgumentParser()
argumentList = [self.queryFofn, self.repoPath, self.outSam,
'--algorithm', 'gmap']
parser, options, _info = parseOptions(argumentList=argumentList,
parser=parser)
service = GMAPService(options, files)
dbRoot, dbName = service._gmapCreateDB(files.targetFileName, True,
self.outDir)
self.assertEqual(path.abspath(dbRoot), path.abspath(self.repoPath))
self.assertEqual(dbName, "gmap_db")
def test_gmapCreateDB_case2(self):
"""Test _gmapCreateDB(refFile, isWithinRepository, tempRootDir).
Condition: the reference is within a reference repository.
"""
# Case 2: the reference is within a reference repository
files = PBAlignFiles()
parser = argparse.ArgumentParser()
argumentList = [
self.queryFofn, self.repoPath, self.outSam, '--algorithm', 'gmap'
]
parser, options, _info = parseOptions(argumentList=argumentList,
parser=parser)
service = GMAPService(options, files)
dbRoot, dbName = service._gmapCreateDB(files.targetFileName, True,
self.outDir)
self.assertEqual(path.abspath(dbRoot), path.abspath(self.repoPath))
self.assertEqual(dbName, "gmap_db")
