view sra.py @ 9:bdb991750a00 draft

debugging automatic SRA build and install

"""
Sra class
"""

import galaxy.datatypes.binary
from galaxy.datatypes.binary import Binary
import data, logging, binascii
from galaxy.datatypes.metadata import MetadataElement
from galaxy.datatypes import metadata
from galaxy.datatypes.sniff import *
from galaxy import eggs
import pkg_resources
pkg_resources.require( 'bx-python' )
import os, subprocess, tempfile
import struct

class Sra( Binary ):
    """ Sequence Read Archive (SRA) """
    file_ext = 'sra'

    def __init__( self, **kwd ):
        Binary.__init__( self, **kwd )
    def sniff( self, filename ):
        """ 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. 
        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 
        """
        try:
            header = open(filename).read(8)
            if binascii.b2a_hex(header) == binascii.hexlify('NCBI.sra'):
                return True
            return False
        except:
            return False
    def set_peek(self, dataset, is_multi_byte=False):
        if not dataset.dataset.purged:
            dataset.peek  = 'Binary sra file'
            dataset.blurb = data.nice_size(dataset.get_size())
        else:
            dataset.peek = 'file does not exist'
            dataset.blurb = 'file purged from disk'
    def display_peek(self, dataset):
        try:
            return dataset.peek
        except:
            return 'Binary sra file (%s)' % ( data.nice_size(dataset.get_size()))

Binary.register_sniffable_binary_format('sra', 'sra', Sra)