Source code for galaxy.util.ucsc

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


[docs]class UCSCLimitException(Exception):
    pass


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

[docs]    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

[docs]    def next(self):
        return self.__next__()

[docs]    def readline(self):
        return next(self)