Mercurial > repos > malex > garli
comparison garli_wrapper.py @ 1:9ce35d2d9937
Uploaded the wrapper
| author | malex |
|---|---|
| date | Fri, 02 Dec 2011 17:07:27 -0500 |
| parents | |
| children |
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| 0:4025ba8b84d6 | 1:9ce35d2d9937 |
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| 1 #!/usr/bin/env python | |
| 2 | |
| 3 """ | |
| 4 Runs Garli-2.0 on a sequence file. | |
| 5 For use with Garli version 2.0 | |
| 6 | |
| 7 usage: garli_wrapper.py config_file best_tree all_trees run_log screen_log out_conf | |
| 8 """ | |
| 9 import os, shutil, subprocess, sys | |
| 10 | |
| 11 def stop_err(msg): | |
| 12 sys.stderr.write("%s\n" % msg) | |
| 13 sys.exit() | |
| 14 | |
| 15 def __main__(): | |
| 16 usage = "usage: %prog input conf btree balltree runlog scrlog outconf" | |
| 17 conf = sys.argv[1] | |
| 18 balltree = 'garli.best.all.tre' | |
| 19 btree = 'garli.best.tre' | |
| 20 runlog = 'garli.log00.log' | |
| 21 scrlog = 'garli.screen.log' | |
| 22 cmd = [] | |
| 23 cmd.append('Garli-2.0') | |
| 24 cmd.append(os.path.basename(conf)) | |
| 25 try: | |
| 26 proc = subprocess.Popen(args=cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE) | |
| 27 except Exception, err: | |
| 28 sys.stderr.write("Error invoking command: \n%s\n\n%s\n" % (cmd, err)) | |
| 29 sys.exit(1) | |
| 30 stdout, stderr = proc.communicate() | |
| 31 return_code = proc.returncode | |
| 32 if return_code: | |
| 33 sys.stdout.write(stdout) | |
| 34 sys.stderr.write(stderr) | |
| 35 sys.stderr.write("Return error code %i from command:\n" % return_code) | |
| 36 sys.stderr.write("%s\n" % cmd) | |
| 37 else: | |
| 38 sys.stdout.write(stdout) | |
| 39 sys.stdout.write(stderr) | |
| 40 try: | |
| 41 shutil.copyfile(os.path.basename(conf), 'garli.conf') | |
| 42 if not os.path.exists(balltree): | |
| 43 bat = open(balltree,'w') | |
| 44 bat.write('Only a single tree was found, so this file does not have any output') | |
| 45 bat.close() | |
| 46 except Exception, err: | |
| 47 sys.stderr.write("Error copying output files: \n%s\n" % err) | |
| 48 if __name__=="__main__": __main__() |