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planemo upload commit d8e0950d53e504e02ee5db43c0804142b14d7fd2-dirty
author crusoe
date Tue, 07 Jul 2015 11:58:46 -0400
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0
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1 """
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2 k-mer count and presence
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3 """
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4
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5 from galaxy.datatypes.binary import Binary
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6 import binascii
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7
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8 import logging
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9
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10 log = logging.getLogger(__name__)
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11
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12
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13 class OxliBinary(Binary):
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14
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15 def __init__(self, **kwd):
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16 Binary.__init__(self, **kwd)
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17
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18 def sniff(self, filename, filetype):
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19 try:
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20 with open(filename) as fileobj:
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21 header = fileobj.read(4)
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22 if binascii.b2a_hex(header) == binascii.hexlify('OXLI'):
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23 fileobj.seek(1)
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24 ftype = fileobj.read(1)
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25 if binascii.b2a_hex(ftype) == filetype:
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26 return True
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27 return False
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28 except IOError:
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29 return False
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30
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31
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32 class Count(OxliBinary):
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33
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34 def __init__(self, **kwd):
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35 OxliBinary.__init__(self, **kwd)
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36
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37 def sniff(self, filename):
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38 return OxliBinary.sniff(self, filename, "01")
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39
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40
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41 class Presence(OxliBinary):
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42
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43 def __init__(self, **kwd):
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44 OxliBinary.__init__(self, **kwd)
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45
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46 def sniff(self, filename):
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47 return OxliBinary.sniff(self, filename, "02")
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48
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49
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50 Binary.register_sniffable_binary_format("ct", "ct", Count)
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51 Binary.register_sniffable_binary_format("pt", "pt", Presence)