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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 SortMeRNA
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5 """
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6
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7 import subprocess
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8 import optparse
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9 import shlex
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10
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11
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12 def main():
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13 """Parse the command line, exectutes SortMeRNA and buildtrie if neeeded."""
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14 #TODO: Put all SortMeRNA options in the command-line parser
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15 parser = optparse.OptionParser()
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16 parser.add_option('--sortmerna', dest='sortmerna_cmd', help='')
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17 parser.add_option('--buildtrie', dest='buildtrie',
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18 default=False, action='store_true', help='')
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19 (options, args) = parser.parse_args()
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20 if not args:
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21 raise Exception('Please provide at least one database')
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22
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23 if options.buildtrie:
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24 buildtrie = 'buildtrie'
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25 for database in args:
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26 run_buildtrie([buildtrie, '--db', database])
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27
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28 if options.sortmerna_cmd:
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29 sortmerna = 'sortmerna'
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30 run_sortmerna([sortmerna] +
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31 shlex.split(options.sortmerna_cmd) +
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32 ['-m', '262144', '-n', str(len(args)), '--db'] +
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33 args)
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34
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35
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36 def run_buildtrie(cmd):
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37 """Run the BuildTrie program."""
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38 try:
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39 stdout_arg = subprocess.PIPE
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40 stderr_arg = subprocess.PIPE
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41 child_process = subprocess.Popen(args=" ".join(cmd), shell=True,
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42 stdin=None, stdout=stdout_arg,
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43 stderr=stderr_arg)
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44 stdout_str, stderr_str = child_process.communicate()
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45 return_code = child_process.returncode
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46 if return_code is not 0:
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47 raise Exception(stderr_str)
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48
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49 except Exception, error:
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50 raise Exception('Error while running Buildtrie:\n' +
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51 '\n'.join([str(error), stdout_str, stderr_str]))
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52
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53
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54 def run_sortmerna(cmd):
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55 """Run the SortMeRNA program."""
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56 try:
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57 stdout_arg = subprocess.PIPE
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58 stderr_arg = subprocess.PIPE
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59 child_process = subprocess.Popen(args=" ".join(cmd), shell=True,
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60 stdin=None, stdout=stdout_arg,
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61 stderr=stderr_arg)
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62 stdout_str, stderr_str = child_process.communicate()
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63 return_code = child_process.returncode
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64 if return_code is not 0:
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65 raise Exception(stderr_str)
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66 except Exception, error:
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67 raise Exception('Error while running SortMeRNA:\n' +
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68 '\n'.join([str(error), stdout_str, stderr_str]))
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69
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70
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71 if __name__ == "__main__":
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72 main()
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