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1 #!/usr/bin/env python
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2
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3 """
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4 Runs Garli-2.0 on a sequence file.
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5 For use with Garli version 2.0
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6
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7 usage: garli_wrapper.py config_file best_tree all_trees run_log screen_log out_conf
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8 """
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9 import os, shutil, subprocess, sys
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10
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11 def stop_err(msg):
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12 sys.stderr.write("%s\n" % msg)
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13 sys.exit()
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14
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15 def __main__():
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16 usage = "usage: %prog input conf btree balltree runlog scrlog outconf"
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17 conf = sys.argv[1]
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18 balltree = 'garli.best.all.tre'
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19 btree = 'garli.best.tre'
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20 runlog = 'garli.log00.log'
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21 scrlog = 'garli.screen.log'
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22 cmd = []
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23 cmd.append('Garli-2.0')
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24 cmd.append(os.path.basename(conf))
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25 try:
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26 proc = subprocess.Popen(args=cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
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27 except Exception, err:
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28 sys.stderr.write("Error invoking command: \n%s\n\n%s\n" % (cmd, err))
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29 sys.exit(1)
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30 stdout, stderr = proc.communicate()
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31 return_code = proc.returncode
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32 if return_code:
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33 sys.stdout.write(stdout)
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34 sys.stderr.write(stderr)
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35 sys.stderr.write("Return error code %i from command:\n" % return_code)
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36 sys.stderr.write("%s\n" % cmd)
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37 else:
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38 sys.stdout.write(stdout)
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39 sys.stdout.write(stderr)
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40 try:
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41 shutil.copyfile(os.path.basename(conf), 'garli.conf')
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42 if not os.path.exists(balltree):
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43 bat = open(balltree,'w')
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44 bat.write('Only a single tree was found, so this file does not have any output')
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45 bat.close()
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46 except Exception, err:
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47 sys.stderr.write("Error copying output files: \n%s\n" % err)
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48 if __name__=="__main__": __main__()
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