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1 """
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2 NCBI sra class
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3 """
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4 import logging
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5 import binascii
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6 from galaxy.datatypes.data import *
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7 from galaxy.datatypes.sniff import *
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8 from galaxy.datatypes.binary import *
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9 from galaxy.datatypes.metadata import *
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10
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11 log = logging.getLogger(__name__)
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12
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13 class sra( Binary ):
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14 """ Sequence Read Archive (SRA) """
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15 file_ext = 'sra'
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16
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17 def __init__( self, **kwd ):
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18 Binary.__init__( self, **kwd )
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19 def sniff( self, filename ):
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20 """ The first 8 bytes of any NCBI sra file is 'NCIB.sra', and the file is binary. EBI and DDBJ files may differ, though EBI and DDBJ
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21 submissions through NCBI (ERR and DRR accessions) read 'NCBI.sra'.
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22 For details about the format, see http://www.ncbi.nlm.nih.gov/books/n/helpsra/SRA_Overview_BK/#SRA_Overview_BK.4_SRA_Data_Structure
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23 """
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24 try:
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25 header = open(filename).read(8)
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26 if binascii.b2a_hex(header) == binascii.hexlify('NCBI.sra'):
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27 return True
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28 else:
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29 return False
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30 except:
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31 return False
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32 def set_peek(self, dataset, is_multi_byte=False):
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33 if not dataset.dataset.purged:
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34 dataset.peek = 'Binary sra file'
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35 dataset.blurb = data.nice_size(dataset.get_size())
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36 else:
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37 dataset.peek = 'file does not exist'
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38 dataset.blurb = 'file purged from disk'
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39 def display_peek(self, dataset):
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40 try:
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41 return dataset.peek
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42 except:
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43 return 'Binary sra file (%s)' % ( data.nice_size(dataset.get_size()))
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44
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45 if hasattr(Binary, 'register_sniffable_binary_format'):
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46 Binary.register_sniffable_binary_format('sra', 'sra', sra)
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