Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/galaxy/util/ucsc.py @ 3:758bc20232e8 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:20:52 -0400
parents 26e78fe6e8c4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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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(object):
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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 self.next()