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annotate galaxy.datatypes.mrh.py @ 10:c11b964e96b3 draft

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planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
author sauria
date Wed, 26 Aug 2015 16:46:18 -0400
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10
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
sauria
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1 from galaxy import eggs
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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2
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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3 import pkg_resources
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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4 pkg_resources.require( "bx-python" )
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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5
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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6 import logging, os, sys, time, sets, tempfile, shutil
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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7 import data
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
sauria
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8 from galaxy import util
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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9 from galaxy.datatypes.sniff import *
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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10 from cgi import escape
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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11 import urllib
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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12 from bx.intervals.io import *
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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13 from galaxy.datatypes import metadata
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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14 from galaxy.datatypes.metadata import MetadataElement
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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15 from galaxy.datatypes.binary import Binary
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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17
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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18 class Mrh( Binary ):
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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19 """Class describing a MRH file"""
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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20 file_ext = "mrh"
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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21
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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22 def sniff( self, filename ):
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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23 # MRH is a binary file type.
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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24 # The first 8 bytes of any mrh file is '42054205'.
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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25 try:
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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26 header = open( filename, 'rb' ).read(8)
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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27 if binascii.b2a_hex( header ) == binascii.hexlify( '42054205' ):
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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28 return True
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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29 return False
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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30 except:
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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31 return False
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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32
c11b964e96b3 planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d
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33 Binary.register_sniffable_binary_format("mrh", "mrh", Mrh)