def openFile(self, dataFile):
# We need to check to see if the path exists here as pysam does
# not throw an error if the index is missing.
if not os.path.exists(self._indexFile):
raise exceptions.FileOpenFailedException(self._indexFile)
try:
return pysam.AlignmentFile(self._dataUrl,
filepath_index=self._indexFile)
except IOError as exception:
# IOError thrown when the index file passed in is not actually
# an index file... may also happen in other cases?
raise exceptions.DataException(exception.message)
def _readFile(self):
if not os.path.exists(self._dataUrl):
raise exceptions.FileOpenFailedException(self._dataUrl)
reader = OboReader(obo_file=self._dataUrl)
ids = set()
for record in reader:
if record.id in ids:
raise exceptions.OntologyFileFormatException(
self._dataUrl, "Duplicate ID {}".format(record.id))
ids.add(record.id)
self._nameIdMap[record.name].append(record.id)
self._sourceVersion = reader.format_version
if len(ids) == 0:
raise exceptions.OntologyFileFormatException(
self._dataUrl, "No valid records found.")
# To get prefix, pull out an ID and parse it.
self._ontologyPrefix = record.id.split(":")[0]
self._sourceVersion = reader.data_version
def getFileHandle(self, dataFile, openMethod):
"""
Returns handle associated to the filename. If the file is
already opened, update its priority in the cache and return
its handle. Otherwise, open the file using openMethod, store
it in the cache and return the corresponding handle.
"""
if dataFile in self._memoTable:
handle = self._memoTable[dataFile]
self._update(dataFile, handle)
return handle
else:
try:
handle = openMethod(dataFile)
except ValueError:
raise exceptions.FileOpenFailedException(dataFile)
self._memoTable[dataFile] = handle
self._add(dataFile, handle)
if len(self._memoTable) > self._maxCacheSize:
dataFile = self._removeLru()
del self._memoTable[dataFile]
return handle