Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/util/ucsc.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 """ |
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2 Utilities for dealing with UCSC data. |
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3 """ |
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4 |
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5 |
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6 class UCSCLimitException(Exception): |
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7 pass |
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8 |
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9 |
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10 class UCSCOutWrapper: |
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11 """File-like object that throws an exception if it encounters the UCSC limit error lines""" |
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12 |
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13 def __init__(self, other): |
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14 self.other = iter(other) |
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15 # Need one line of lookahead to be sure we are hitting the limit message |
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16 self.lookahead = None |
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17 |
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18 def __iter__(self): |
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19 return self |
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20 |
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21 def __next__(self): |
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22 if self.lookahead is None: |
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23 line = next(self.other) |
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24 else: |
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25 line = self.lookahead |
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26 self.lookahead = None |
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27 if line.startswith("----------"): |
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28 next_line = next(self.other) |
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29 if next_line.startswith("Reached output limit"): |
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30 raise UCSCLimitException(next_line.strip()) |
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31 else: |
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32 self.lookahead = next_line |
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33 return line |
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34 |
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35 def next(self): |
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36 return self.__next__() |
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37 |
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38 def readline(self): |
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39 return next(self) |