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