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annotate sra.py @ 8:e40b9582d80f draft

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debugging automatic SRA build and install
author Matt Shirley <mdshw5@gmail.com>
date Mon, 17 Jun 2013 14:00:25 -0400
parents 28fda7631857
children b77840618b8f
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1 """
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2 Sra class
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3 """
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4
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5 import galaxy.datatypes.binary
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6 from galaxy.datatypes.binary import Binary
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7 import data, logging, binascii
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8 from galaxy.datatypes.metadata import MetadataElement
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9 from galaxy.datatypes import metadata
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10 from galaxy.datatypes.sniff import *
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11 from galaxy import eggs
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12 import pkg_resources
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13 pkg_resources.require( 'bx-python' )
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14 import os, subprocess, tempfile
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15 import struct
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16
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17 class Sra( Binary ):
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18 """ Sequence Read Archive (SRA) """
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19 file_ext = 'sra'
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20
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21 def __init__( self, **kwd ):
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22 Binary.__init__( self, **kwd )
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23 def sniff( self, filename ):
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24 """ The first 8 bytes of any NCBI sra file is 'NCIB.sra', and the file is binary. Not sure if EBI and DDBJ files may differ.
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25 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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26 """
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27 try:
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28 header = open(filename).read(8)
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29 if binascii.b2a_hex(header) == binascii.hexlify('NCBI.sra'):
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30 return True
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31 return False
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32 except:
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33 return False
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34 def set_peek(self, dataset, is_multi_byte=False):
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35 if not dataset.dataset.purged:
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36 dataset.peek = 'Binary sra file'
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37 dataset.blurb = data.nice_size(dataset.get_size())
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38 else:
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39 dataset.peek = 'file does not exist'
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40 dataset.blurb = 'file purged from disk'
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41 def display_peek(self, dataset):
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42 try:
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43 return dataset.peek
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44 except:
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45 return 'Binary sra file (%s)' % ( data.nice_size(dataset.get_size()))
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46
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47 Binary.register_sniffable_binary_format('sra', 'sra', Sra)