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annotate sra.py @ 0:9f74a22d2060 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
author mvdbeek
date Wed, 04 Nov 2015 06:57:32 -0500
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9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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1 """
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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2 NCBI sra class
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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3 """
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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4 import logging
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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5 import binascii
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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6 from galaxy.datatypes.data import nice_size
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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7 from galaxy.datatypes.binary import Binary
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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8
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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9 log = logging.getLogger(__name__)
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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10
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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11 class Sra(Binary):
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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12 """ Sequence Read Archive (SRA) """
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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13 file_ext = 'sra'
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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14
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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15 def __init__( self, **kwd ):
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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16 Binary.__init__( self, **kwd )
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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17
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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18 def sniff( self, filename ):
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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19 """ The first 8 bytes of any NCBI sra file is 'NCBI.sra', and the file is binary.
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
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
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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21 """
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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22 try:
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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23 header = open(filename).read(8)
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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24 if binascii.b2a_hex(header) == binascii.hexlify('NCBI.sra'):
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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25 return True
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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26 else:
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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27 return False
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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28 except:
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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29 return False
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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30
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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31 def set_peek(self, dataset, is_multi_byte=False):
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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32 if not dataset.dataset.purged:
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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33 dataset.peek = 'Binary sra file'
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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34 dataset.blurb = nice_size(dataset.get_size())
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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35 else:
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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36 dataset.peek = 'file does not exist'
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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37 dataset.blurb = 'file purged from disk'
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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38
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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39 def display_peek(self, dataset):
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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40 try:
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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41 return dataset.peek
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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42 except:
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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43 return 'Binary sra file (%s)' % (nice_size(dataset.get_size()))
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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44
9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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45 Binary.register_sniffable_binary_format('sra', 'sra', Sra)