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annotate velvetg_wrapper.py @ 0:08256557922f draft

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planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
author devteam
date Tue, 13 Oct 2015 16:38:28 -0400
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08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
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1 #!/usr/bin/env python
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2
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3 """
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4 Classes encapsulating decypher tool.
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5 James E Johnson - University of Minnesota
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6 """
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7 import os
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8 import sys
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9 import subprocess
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10
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11 assert sys.version_info[:2] >= ( 2, 4 )
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12
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13 def stop_err( msg ):
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14 sys.stderr.write( "%s\n" % msg )
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15 sys.exit()
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17
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18 def __main__():
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19 #Parse Command Line
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20 working_dir = sys.argv[1]
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21 inputs = ' '.join(sys.argv[2:])
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22 for _ in ('Roadmaps', 'Sequences'):
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23 os.symlink(os.path.join(working_dir, _), _)
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24 cmdline = 'velvetg . %s' % (inputs)
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25 print "Command to be executed: %s" % cmdline
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26 try:
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27 proc = subprocess.Popen( args=cmdline, shell=True, stderr=subprocess.PIPE )
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28 returncode = proc.wait()
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29 # get stderr, allowing for case where it's very large
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30 stderr = ''
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31 buffsize = 1048576
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32 try:
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33 while True:
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34 stderr += proc.stderr.read( buffsize )
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35 if not stderr or len( stderr ) % buffsize != 0:
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36 break
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37 except OverflowError:
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38 pass
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39 if returncode != 0:
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40 raise Exception, stderr
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41 except Exception, e:
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42 stop_err( 'Error running velvetg ' + str( e ) )
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43
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44
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45 if __name__ == "__main__":
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46 __main__()