Mercurial > repos > bgruening > upload_testing
comparison reverse.py @ 110:fa6ef7619bbd draft default tip
Uploaded
| author | bgruening |
|---|---|
| date | Mon, 26 Jan 2015 13:10:16 -0500 |
| parents | 89dd3b812906 |
| children |
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| 109:89dd3b812906 | 110:fa6ef7619bbd |
|---|---|
| 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() | |
| 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) | |
| 14 | |
| 15 | |
| 16 def _run_shell(command): | |
| 17 if DEBUG: | |
| 18 print "Running shell command %s" % command | |
| 19 _exec(command) | |
| 20 | |
| 21 | |
| 22 def _run_dbtoolkit(java_class, command, args): | |
| 23 command_prefix = "java -cp %s" % _dbtoolkit_jar_path( args.script_path ) | |
| 24 _exec("%s %s %s" % (command_prefix, java_class, command)) | |
| 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() |