def __init__(self, f, fname, default_sample_id): TextParser.__init__(self, f, fname, default_sample_id) self.__format = None # Metadata and comments line = self._readline() while len(line) > 0 and line.startswith("#"): if line.startswith("##fileformat="): self.__format = line[13:] line = self._readline() if len(line) > 0: # Header column_indices = {} columns = line.rstrip().split("\t") self._col_size = len(columns) for i, name in enumerate(columns): name = name.lower() if name in _COLUMNS: column_indices[name] = i try: self._col_name_indices = column_indices self._col_indices = [column_indices[name] for name in _COLUMNS] except KeyError as ex: raise ParserException("Header column not found: {0}".format(ex.args[0]), self._location()) else: raise ParserException("Header not found", (self._fname))
def __init__(self, f, fname, default_sample_id): TextParser.__init__(self, f, fname, default_sample_id) self.__format = None # Metadata and comments line = self._readline() while len(line) > 0 and line.startswith("#"): if line.startswith("##INDIVIDUAL="): self._default_sample_id = line[13:] elif line.startswith("##fileformat="): self.__format = line[13:] line = self._readline() if len(line) > 0: # First line self._queue_line(line)
def __init__(self, f, fname, default_sample_id): TextParser.__init__(self, f, fname, default_sample_id)