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(self):
"""Test TempFileManager all functions."""
t = TempFileManager()
t.SetRootDir("/scratch")
newFN = t.RegisterNewTmpFile()
self.assertTrue(path.isfile(newFN))
existingDir = t.RegisterExistingTmpFile("/tmp", isDir=True)
self.assertTrue(path.isdir(existingDir))
with self.assertRaises(IOError) as cm:
t.RegisterExistingTmpFile("filethatdoesnotexist")
newDN = t.RegisterNewTmpFile(isDir=True)
self.assertTrue(path.isdir(newDN))
self.assertTrue(t._isRegistered(newDN))
newTxt = t.RegisterNewTmpFile(suffix=".txt")
self.assertTrue(newTxt.endswith(".txt"))
t.SetRootDir("~/tmp/")
t.CleanUp()
self.assertFalse(path.exists(newFN))
self.assertFalse(path.exists(newDN))
self.assertEqual(t.fileDB, [])
self.assertEqual(t.dirDB, [])
def __init__(self, options, fileNames, tempFileManager=None):
"""Initialize an AlignSerivce object.
Need to resolve options specified within algorithmOptions;
patch default options if not specified by the user
inherit or initialize a tempory file manager
Input:
options : options parsed from (a list of arguments and
a config file if --configFile is specified).
fileNames : an object of PBAlignFiles
tempFileManager: a temporary file manager. If it is None,
create a new temporary file manager.
"""
self._options = options
# Verify and assign input & output files.
self._fileNames = fileNames
self._fileNames.SetInOutFiles(self._options.inputFileName,
self._options.referencePath,
self._options.outputFileName,
self._options.regionTable,
self._options.pulseFile)
# Resolve options specified within --algorithmOptions with
# options parsed from the argument list (e.g. the command-line)
# or a config file.
self._options = self._resolveAlgorithmOptions(self._options,
self._fileNames)
# Patch PBalign default options if they havn't been specified yet.
self._options = importDefaultOptions(self._options)[0]
if tempFileManager is None:
self._tempFileManager = TempFileManager(self._options.tmpDir)
else:
self._tempFileManager = tempFileManager
self._tempFileManager.SetRootDir(self._options.tmpDir)
# self.args is finalized.
logging.debug("Parsed arguments considering configFile and " +
"algorithmOptions: " + str(self._options))