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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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12 format_args = (options.input, options.output)
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13 _run_shell("cat '%s' > '%s'" % format_args)
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14 _run_dbtoolkit("com.compomics.dbtoolkit.toolkit.ReverseFASTADB", "'%s' | head --lines -4 >> '%s'" % \
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15 format_args)
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16
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17
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18 def _run_shell(command):
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19 if DEBUG:
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20 print "Running shell command %s" % command
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21 _exec(command)
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22
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23
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24 def _run_dbtoolkit(java_class, args):
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25 command_prefix = "java -cp %s" % _dbtoolkit_jar_path( args.script_path )
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26 _exec("%s %s %s" % (command_prefix, java_class, args))
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27
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28
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29 def _dbtoolkit_jar_path( script_path ):
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30 jar_path = join(script_path, "dbtoolkit-4.2", "dbtoolkit-4.2.jar")
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31 return jar_path
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32
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33 def _exec(command):
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34 proc = subprocess.Popen(args=command, shell=True)
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35 return_code = proc.wait()
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36 if return_code != 0:
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37 print "Error executing command [%s], return code is %d" % (command, return_code)
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38 sys.exit(return_code)
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39
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40
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41 def _parse_args():
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42 parser = OptionParser()
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43 parser.add_option("-i", "--input")
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44 parser.add_option("-o", "--output")
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45 parser.add_option("-s", "--script_path")
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46 return parser.parse_args()
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47
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48
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49 if __name__ == "__main__":
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50 main()
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