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Source code for galaxy.util.ucsc

Utilities for dealing with UCSC data.

[docs]class UCSCLimitException(Exception): pass
[docs]class UCSCOutWrapper(object): """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
[docs] def next(self): if self.lookahead is None: line = self.other.next() else: line = self.lookahead self.lookahead = None if line.startswith("----------"): next_line = self.other.next() if next_line.startswith("Reached output limit"): raise UCSCLimitException(next_line.strip()) else: self.lookahead = next_line return line
[docs] def readline(self): return self.next()