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1 """
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2 Cuffquant format class
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3 """
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4 import logging
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5 import re
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6 import binascii
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7
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8 from galaxy.datatypes.sniff import *
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9 from galaxy.datatypes import data
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10 from galaxy.datatypes.data import Binary
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11 #from galaxy.datatypes.binary import Binary
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12 #from galaxy.datatypes.tabular import Tabular
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13 #from galaxy.datatypes.interval import Gff
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14
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15 log = logging.getLogger(__name__)
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16
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17 class Cuffquant( Binary ):
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18 """Class describing a CuffQuant output file"""
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19 file_ext = "cxb"
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20 def sniff(self,filename):
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21 # cuffquant cxb file is not documented. the file seems to start with 'serialization::'
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22 try:
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23 header = open(filename).read(23)
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24 if header == 'serialization::':
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25 return True
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26 return False
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27 except:
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28 return False
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29
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30 def set_peek( self, dataset, is_multi_byte=False):
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31 if not dataset.dataset.purged:
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32 dataset.peek = 'Cuffquant cxb file'
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33 dataset.blurb = data.nice_size( dataset.get_size())
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34 else:
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35 dataset.peek = 'file does not exist'
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36 dataset.blurb = 'file purged from disk'
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37 def display_peek (self,dataset):
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38 try:
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39 return dataset.peek
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40 except:
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41 return "Cuffquant output file (%s)" % ( data.nice_size( dataset.get_size() ) )
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42
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43 if hasattr(Binary, 'register_sniffable_binary_format'):
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44 Binary.register_sniffable_binary_format('cxb', 'cxb', Cuffquant)
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