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