Mercurial > repos > greg > plant_tribes_gene_family_aligner

comparison run_pasta.py @ 0:7ba9469800b9 draft

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author greg
date Thu, 08 Jun 2017 12:46:20 -0400
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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 as 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)