def setUp(self):
self.inCmpFile = path.join(DATA_DIR, "testforquiver.cmp.h5")
self.outCmpFile = mkstemp(suffix=".cmp.h5")[1]
copyfile(self.inCmpFile, self.outCmpFile)
self.basFile = path.join(DATA_DIR, "lambda_bax.fofn")
refpath = "/pbi/dept/secondary/siv/references/lambda/"
self.fileNames = PBAlignFiles()
self.fileNames.SetInOutFiles(self.basFile, refpath, self.outCmpFile,
None, None)
self.options = Opt()
self.obj = ForQuiverService(self.fileNames, self.options)
def test_setInOutFiles(self):
"""Test PBAlignFiles.SetInOutFiles()."""
p = PBAlignFiles()
self.assertIsNone(p.inputFileName)
self.assertIsNone(p.outputFileName)
self.assertIsNone(p.referencePath)
p.SetInOutFiles(self.inputFileName, self.referenceFile,
self.outputFileName, None)
self.assertTrue(filecmp.cmp(p.inputFileName, self.inputFileName))
self.assertTrue(filecmp.cmp(p.referencePath, self.referenceFile))
self.assertTrue(filecmp.cmp(p.targetFileName, self.referenceFile))
self.assertTrue(filecmp.cmp(p.outputFileName, self.outputFileName))
self.assertIsNone(p.regionTable)
def __init__(self,
args=None,
argumentList=(),
output_dataset_type=AlignmentSet):
"""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."
if args is None: # FIXME unit testing hack
args = get_contract_parser().arg_parser.parser.parse_args(
argumentList)
self.args = args
# 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 = 1 if (self.args.verbosity is None) else \
# (int(self.args.verbosity) / 2 + 1)
super(PBAlignRunner, self).__init__(desc)
self._output_dataset_type = output_dataset_type
self._alnService = None
self._filterService = None
self.fileNames = PBAlignFiles()
self._tempFileManager = TempFileManager()
def test_init_region_table(self):
"""Test PBAlignFiles.__init__() with a region table."""
# With an artifical region table
regionTable = path.join(self.rootDir, "data/lambda.rgn.h5")
p = PBAlignFiles(self.inputFileName, self.referenceFile,
self.outputFileName, regionTable)
self.assertTrue(filecmp.cmp(p.regionTable, regionTable))
def test_init(self):
"""Test PBAlignFiles.__init__()."""
# Without region table
p = PBAlignFiles(self.inputFileName, self.referenceFile,
self.outputFileName)
self.assertTrue(filecmp.cmp(p.inputFileName, self.inputFileName))
self.assertTrue(filecmp.cmp(p.referencePath, self.referenceFile))
self.assertTrue(filecmp.cmp(p.targetFileName, self.referenceFile))
self.assertTrue(filecmp.cmp(p.outputFileName, self.outputFileName))
self.assertIsNone(p.regionTable)
def test_init(self):
"""Test PBAlignFiles.__init__() with a reference repository."""
# Without region table
p = PBAlignFiles(self.inputFileName, self.referencePath,
self.outputFileName)
self.assertTrue(filecmp.cmp(p.inputFileName, self.inputFileName))
self.assertTrue(p.referencePath,
path.abspath(path.expanduser(self.referencePath)))
self.assertTrue(filecmp.cmp(p.targetFileName, self.targetFileName))
self.assertTrue(filecmp.cmp(p.outputFileName, self.outputFileName))
self.assertIsNone(p.regionTable)
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")
class Test_ForQuiverService(unittest.TestCase):
"""Test pbalign.forquiverservice.forquiver."""
def setUp(self):
self.inCmpFile = path.join(DATA_DIR, "testforquiver.cmp.h5")
self.outCmpFile = mkstemp(suffix=".cmp.h5")[1]
copyfile(self.inCmpFile, self.outCmpFile)
self.basFile = path.join(DATA_DIR, "lambda_bax.fofn")
refpath = "/pbi/dept/secondary/siv/references/lambda/"
self.fileNames = PBAlignFiles()
self.fileNames.SetInOutFiles(self.basFile, refpath, self.outCmpFile,
None, None)
self.options = Opt()
self.obj = ForQuiverService(self.fileNames, self.options)
def tearDown(self):
remove(self.outCmpFile)
def test_run(self):
"""Test ForQuiverService.__init__()."""
self.obj.run()