Warning

This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

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()