Mercurial > repos > greg > phylogenomics_analysis
comparison run_pasta.py @ 102:3348b5ae153b draft
Uploaded
| author | greg |
|---|---|
| date | Mon, 27 Mar 2017 10:50:23 -0400 |
| parents | 8529a3c95c2b |
| children |
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| 101:9c6b468d8db2 | 102:3348b5ae153b |
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| 1 #! /usr/bin/env python | |
| 2 | |
| 3 """Main script of PASTA in command-line mode - this simply invokes the main | |
| 4 function found in pasta/mainpasta.py | |
| 5 """ | |
| 6 | |
| 7 # This file is part of PASTA which is forked from SATe | |
| 8 | |
| 9 # PASTA like SATe is free software: you can redistribute it and/or modify | |
| 10 # it under the terms of the GNU General Public License as published by | |
| 11 # the Free Software Foundation, either version 3 of the License, or | |
| 12 # (at your option) any later version. | |
| 13 # | |
| 14 # This program is distributed in the hope that it will be useful, | |
| 15 # but WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 16 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
| 17 # GNU General Public License for more details. | |
| 18 # | |
| 19 # You should have received a copy of the GNU General Public License | |
| 20 # along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 21 | |
| 22 # Jiaye Yu and Mark Holder, University of Kansas | |
| 23 | |
| 24 if __name__ == "__main__": | |
| 25 import os | |
| 26 import sys | |
| 27 from pasta.mainpasta import pasta_main | |
| 28 from pasta import MESSENGER | |
| 29 sys.setrecursionlimit(100000) | |
| 30 _PASTA_DEBUG = os.environ.get('PASTA_DEBUG') | |
| 31 _DEVELOPER = _PASTA_DEBUG and _PASTA_DEBUG != '0' | |
| 32 | |
| 33 if not _DEVELOPER: | |
| 34 _PASTA_DEVELOPER = os.environ.get('PASTA_DEVELOPER') | |
| 35 _DEVELOPER = _PASTA_DEVELOPER and _PASTA_DEVELOPER != '0' | |
| 36 try: | |
| 37 rc, temp_dir, temp_fs = pasta_main() | |
| 38 if not rc: | |
| 39 raise ValueError("Unknown PASTA execution error") | |
| 40 if (temp_dir is not None) and (os.path.exists(temp_dir)): | |
| 41 MESSENGER.send_info("Note that temporary files from the run have not been deleted, they can be found in:\n '%s'\n" % temp_dir) | |
| 42 if sys.platform.lower().startswith('darwin') and ("'" not in temp_dir): | |
| 43 MESSENGER.send_info(''' | |
| 44 If you cannot see this directory in the Finder application, you may want to use | |
| 45 the 'open' command executed from a Terminal. You can do this by launching the | |
| 46 /Applications/Utilities/Terminal program and then typing | |
| 47 | |
| 48 open '%s' | |
| 49 | |
| 50 followed by a return at the prompt. If the argument to the open command is a | |
| 51 directory, then it should open a Finder window in the directory (even if that | |
| 52 directory is hidden by default). | |
| 53 ''' % temp_dir) | |
| 54 except Exception, x: | |
| 55 if _DEVELOPER: | |
| 56 raise | |
| 57 message = "PASTA is exiting because of an error:\n%s " % str(x) | |
| 58 try: | |
| 59 from pasta import MESSENGER | |
| 60 MESSENGER.send_error(message) | |
| 61 except: | |
| 62 sys.stderr.write(message) | |
| 63 sys.exit(1) |
