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105
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1 #!/usr/bin/env python
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2 from os.path import join
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3 import sys
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4 from optparse import OptionParser
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5 from ConfigParser import SafeConfigParser
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6 import subprocess
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7
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8 DEBUG = False
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9
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10 def main():
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11 (options, args) = _parse_args()
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108
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12 _run_shell("cat '%s' > '%s'" % (options.input, options.output))
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13 _run_dbtoolkit("com.compomics.dbtoolkit.toolkit.ReverseFASTADB", "'%s' | head --lines -4 >> '%s'" % (options.input, options.output), options)
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105
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14
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15
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16 def _run_shell(command):
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17 if DEBUG:
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18 print "Running shell command %s" % command
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19 _exec(command)
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20
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21
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22 def _run_dbtoolkit(java_class, args):
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23 command_prefix = "java -cp %s" % _dbtoolkit_jar_path( args.script_path )
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24 _exec("%s %s %s" % (command_prefix, java_class, args))
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25
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26
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27 def _dbtoolkit_jar_path( script_path ):
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28 jar_path = join(script_path, "dbtoolkit-4.2", "dbtoolkit-4.2.jar")
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29 return jar_path
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30
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31 def _exec(command):
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32 proc = subprocess.Popen(args=command, shell=True)
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33 return_code = proc.wait()
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34 if return_code != 0:
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35 print "Error executing command [%s], return code is %d" % (command, return_code)
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36 sys.exit(return_code)
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37
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38
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39 def _parse_args():
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40 parser = OptionParser()
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41 parser.add_option("-i", "--input")
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42 parser.add_option("-o", "--output")
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43 parser.add_option("-s", "--script_path")
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44 return parser.parse_args()
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45
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46
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47 if __name__ == "__main__":
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48 main()
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