|
105
|
1 #!/usr/bin/env python
|
|
|
2 from os.path import join
|
|
|
3 import sys
|
|
|
4 from optparse import OptionParser
|
|
|
5 from ConfigParser import SafeConfigParser
|
|
|
6 import subprocess
|
|
|
7
|
|
|
8 DEBUG = False
|
|
|
9
|
|
|
10 def main():
|
|
|
11 (options, args) = _parse_args()
|
|
108
|
12 _run_shell("cat '%s' > '%s'" % (options.input, options.output))
|
|
|
13 _run_dbtoolkit("com.compomics.dbtoolkit.toolkit.ReverseFASTADB", "'%s' | head --lines -4 >> '%s'" % (options.input, options.output), options)
|
|
105
|
14
|
|
|
15
|
|
|
16 def _run_shell(command):
|
|
|
17 if DEBUG:
|
|
|
18 print "Running shell command %s" % command
|
|
|
19 _exec(command)
|
|
|
20
|
|
|
21
|
|
109
|
22 def _run_dbtoolkit(java_class, command, args):
|
|
105
|
23 command_prefix = "java -cp %s" % _dbtoolkit_jar_path( args.script_path )
|
|
109
|
24 _exec("%s %s %s" % (command_prefix, java_class, command))
|
|
105
|
25
|
|
|
26
|
|
|
27 def _dbtoolkit_jar_path( script_path ):
|
|
|
28 jar_path = join(script_path, "dbtoolkit-4.2", "dbtoolkit-4.2.jar")
|
|
|
29 return jar_path
|
|
|
30
|
|
|
31 def _exec(command):
|
|
|
32 proc = subprocess.Popen(args=command, shell=True)
|
|
|
33 return_code = proc.wait()
|
|
|
34 if return_code != 0:
|
|
|
35 print "Error executing command [%s], return code is %d" % (command, return_code)
|
|
|
36 sys.exit(return_code)
|
|
|
37
|
|
|
38
|
|
|
39 def _parse_args():
|
|
|
40 parser = OptionParser()
|
|
|
41 parser.add_option("-i", "--input")
|
|
|
42 parser.add_option("-o", "--output")
|
|
|
43 parser.add_option("-s", "--script_path")
|
|
|
44 return parser.parse_args()
|
|
|
45
|
|
|
46
|
|
|
47 if __name__ == "__main__":
|
|
|
48 main()
|
