class ForQuiverService(object):
""" Uses SortService, LoadPulsesService, RepackService to post process
a cmp.h5 file so that the file can be used by quiver directly.
"""
@property
def name(self):
"""Name of ForQuiverService."""
return "ForQuiverService"
def __init__(self, fileNames, options):
"""Initialize a ForQuiverService object.
Input:
fileNames : pbalign file names
options : pbalign options
"""
self.fileNames = fileNames
self.options = options
self._loadpulsesService = LoadPulsesService(
self.fileNames.pulseFileName,
self.fileNames.outputFileName,
self.options)
self._sortService = SortService(
self.fileNames.outputFileName,
self.options)
self._repackService = RepackService(
self.fileNames.outputFileName,
self.fileNames.outputFileName + ".TMP")
def run(self):
""" Run the ForQuiver service."""
logging.info(self.name + ": Sort.")
self._sortService.checkAvailability()
self._sortService.run()
logging.info(self.name + ": LoadPulses.")
self._loadpulsesService.checkAvailability()
self._loadpulsesService.run()
logging.info(self.name + ": Repack.")
self._repackService.checkAvailability()
self._repackService.run()
def setUp(self):
"""Set up tests."""
self.rootDir = "/mnt/secondary-siv/secondarytest/" + \
"testdata/BlasrTestData/pbalign"
self.inCmpFile = path.join(self.rootDir, "data/testloadpulses.cmp.h5")
#self.outCmpFile = path.join(self.rootDir, "out/testloadpulses.cmp.h5")
self.outCmpFile = mkstemp(suffix=".cmp.h5")[1]
self.basFile = path.join(self.rootDir, "data/lambda_bax.fofn")
copyfile(self.inCmpFile, self.outCmpFile)
self.options = Namespace(metrics="DeletionQV", byread=False)
self.obj = LoadPulsesService(self.basFile,
self.outCmpFile, self.options)
def __init__(self, fileNames, options):
"""Initialize a ForQuiverService object.
Input:
fileNames : pbalign file names
options : pbalign options
"""
self.fileNames = fileNames
self.options = options
self._loadpulsesService = LoadPulsesService(
self.fileNames.pulseFileName,
self.fileNames.outputFileName,
self.options)
self._sortService = SortService(
self.fileNames.outputFileName,
self.options)
self._repackService = RepackService(
self.fileNames.outputFileName,
self.fileNames.outputFileName + ".TMP")
class Test_LoadPulsesService(unittest.TestCase):
"""Test pbtools.pbalign.forquiverservice.loadpulses."""
def setUp(self):
"""Set up tests."""
self.rootDir = "/mnt/secondary-siv/secondarytest/" + \
"testdata/BlasrTestData/pbalign"
self.inCmpFile = path.join(self.rootDir, "data/testloadpulses.cmp.h5")
#self.outCmpFile = path.join(self.rootDir, "out/testloadpulses.cmp.h5")
self.outCmpFile = mkstemp(suffix=".cmp.h5")[1]
self.basFile = path.join(self.rootDir, "data/lambda_bax.fofn")
copyfile(self.inCmpFile, self.outCmpFile)
self.options = Namespace(metrics="DeletionQV", byread=False)
self.obj = LoadPulsesService(self.basFile,
self.outCmpFile, self.options)
def tearDown(self):
remove(self.outCmpFile)
def test_run(self):
"""Test LoadPulsesService.__init__()."""
_output, errCode, _errMsg = self.obj.run()
self.assertEqual(errCode, 0)
