Mercurial > repos > shellac > guppy_basecaller
comparison env/lib/python3.7/site-packages/galaxy/util/ucsc.py @ 2:6af9afd405e9 draft
"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"
| author | shellac |
|---|---|
| date | Thu, 14 May 2020 14:56:58 -0400 |
| parents | 26e78fe6e8c4 |
| children |
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| 1:75ca89e9b81c | 2:6af9afd405e9 |
|---|---|
| 1 """ | |
| 2 Utilities for dealing with UCSC data. | |
| 3 """ | |
| 4 | |
| 5 | |
| 6 class UCSCLimitException(Exception): | |
| 7 pass | |
| 8 | |
| 9 | |
| 10 class UCSCOutWrapper(object): | |
| 11 """File-like object that throws an exception if it encounters the UCSC limit error lines""" | |
| 12 | |
| 13 def __init__(self, other): | |
| 14 self.other = iter(other) | |
| 15 # Need one line of lookahead to be sure we are hitting the limit message | |
| 16 self.lookahead = None | |
| 17 | |
| 18 def __iter__(self): | |
| 19 return self | |
| 20 | |
| 21 def __next__(self): | |
| 22 if self.lookahead is None: | |
| 23 line = next(self.other) | |
| 24 else: | |
| 25 line = self.lookahead | |
| 26 self.lookahead = None | |
| 27 if line.startswith("----------"): | |
| 28 next_line = next(self.other) | |
| 29 if next_line.startswith("Reached output limit"): | |
| 30 raise UCSCLimitException(next_line.strip()) | |
| 31 else: | |
| 32 self.lookahead = next_line | |
| 33 return line | |
| 34 | |
| 35 def next(self): | |
| 36 return self.__next__() | |
| 37 | |
| 38 def readline(self): | |
| 39 return self.next() |