def __init__(self, file_spec, processor):
super(FastaLikeFileParser, self).__init__()
self.state = ParserState.defline
self.handle = opener(file_spec)
self.defline = None
self.sequence_chunks = []
self.processor = processor
def __init__(self, stream):
self.graph = {}
self.state = START
self.handle = opener(stream, "r")
self.counter = 0
self.repeats = {}
self.buffer = defaultdict(list)
self.root = None
self._iter = None
def __init__(self, stream, structure_class=Glycan):
'''
Creates a parser of condensed GlycoCT.
Parameters
----------
stream: basestring or file-like
A path to a file or a file-like object to be processed
'''
self.graph = {}
self.handle = opener(stream, "r")
self.state = START
self.current_repeat = None
self.in_repeat = False
self.repeats = {}
self.postponed = []
self.root = None
self._iter = None
self.structure_class = structure_class
def make_pipeline(self):
self.loader = TextFileGlycanCompositionLoader(
opener(self.glycan_file, 'r'))
self.transformer = GlycanTransformer(self.loader, self.reduction,
self.derivatization)
def make_pipeline(self):
self.loader = TextFileGlycanCompositionLoader(opener(self.glycan_file, 'r'))
self.transformer = GlycanTransformer(self.loader, self.reduction, self.derivatization)
def read(path):
return AnnotatedMGFDeserializer(opener(path, 'rb'))
def default_serializer(obj, file_path):
try:
pickle.dump(obj, opener(file_path, "wb"))
except Exception, e:
decon_io_logger.warning("Failed to open %s for default_serializer, for %s", file_path, obj, exc_info=e)
def default_loader(file_path):
try:
return pickle.load(opener(file_path, "rb"))
except Exception, e:
decon_io_logger.warning("Failed to open %s for default_loader", file_path, exc_info=e)
def _load(self, file_path):
self.data = pickle.load(opener(file_path))
def __init__(self, file_spec, processor):
super(StructurePerLineParser, self).__init__()
self.handle = opener(file_spec)
self.processor = processor
