Mercurial > repos > shellac > guppy_basecaller

"""
Utilities for dealing with UCSC data.
"""


class UCSCLimitException(Exception):
    pass


class UCSCOutWrapper(object):
    """File-like object that throws an exception if it encounters the UCSC limit error lines"""

    def __init__(self, other):
        self.other = iter(other)
        # Need one line of lookahead to be sure we are hitting the limit message
        self.lookahead = None

    def __iter__(self):
        return self

    def __next__(self):
        if self.lookahead is None:
            line = next(self.other)
        else:
            line = self.lookahead
            self.lookahead = None
        if line.startswith("----------"):
            next_line = next(self.other)
            if next_line.startswith("Reached output limit"):
                raise UCSCLimitException(next_line.strip())
            else:
                self.lookahead = next_line
        return line

    def next(self):
        return self.__next__()

    def readline(self):
        return self.next()
author	shellac
date	Sat, 02 May 2020 07:14:21 -0400
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