Mercurial > repos > mvdbeek > sra_tools

annotate sra.py @ 1:4965e09adc02 draft

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planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181-dirty
author mvdbeek
date Fri, 25 Sep 2015 10:20:20 -0400
parents 68527898a9ea
children
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68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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1 """
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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2 NCBI sra class
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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3 """
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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4 import logging
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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5 import binascii
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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6 from galaxy.datatypes.data import nice_size
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
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7 from galaxy.datatypes.binary import Binary
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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9 log = logging.getLogger(__name__)
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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11 class Sra(Binary):
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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12 """ Sequence Read Archive (SRA) """
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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13 file_ext = 'sra'
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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15 def __init__( self, **kwd ):
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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16 Binary.__init__( self, **kwd )
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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18 def sniff( self, filename ):
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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19 """ The first 8 bytes of any NCBI sra file is 'NCBI.sra', and the file is binary.
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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20 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
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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21 """
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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22 try:
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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23 header = open(filename).read(8)
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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24 if binascii.b2a_hex(header) == binascii.hexlify('NCBI.sra'):
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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25 return True
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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26 else:
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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27 return False
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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28 except:
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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29 return False
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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31 def set_peek(self, dataset, is_multi_byte=False):
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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32 if not dataset.dataset.purged:
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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33 dataset.peek = 'Binary sra file'
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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34 dataset.blurb = nice_size(dataset.get_size())
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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35 else:
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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36 dataset.peek = 'file does not exist'
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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37 dataset.blurb = 'file purged from disk'
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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38
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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39 def display_peek(self, dataset):
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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40 try:
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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41 return dataset.peek
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
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42 except:
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
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43 return 'Binary sra file (%s)' % (nice_size(dataset.get_size()))
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
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44
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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45 Binary.register_sniffable_binary_format('sra', 'sra', Sra)