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 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")
def __init__(self, argumentList):
"""Initialize a PBAlignRunner object.
argumentList is a list of arguments, such as:
['--debug', '--maxHits', '10', 'in.fasta', 'ref.fasta', 'out.sam']
"""
desc = "Utilities for aligning PacBio reads to reference sequences."
super(PBAlignRunner, self).__init__(desc)
self._argumentList = argumentList
self._alnService = None
self._filterService = None
self.fileNames = PBAlignFiles()
self._tempFileManager = TempFileManager()
self.parser, self.args, _infoMsg = parseOptions(
argumentList=self._argumentList, parser=self.parser)
# args.verbosity is computed by counting # of 'v's in '-vv...'.
# However in parseOptions, arguments are parsed twice to import config
# options and then overwrite them with argumentList (e.g. command-line)
# options.
self.args.verbosity = 0 if (self.args.verbosity is None) else \
int(self.args.verbosity) / 2