Mercurial > repos > charles-bernard > alfa
comparison ALFA/ALFA_wrapper.py @ 26:f1a20d50c495 draft
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| author | charles-bernard |
|---|---|
| date | Mon, 31 Oct 2016 14:06:36 -0400 |
| parents | 1714165f5df0 |
| children | 2496883e588b |
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| 25:37fce32b0298 | 26:f1a20d50c495 |
|---|---|
| 38 parser.add_argument('--categories_depth', dest='categories_depth', action='store', nargs=1, default=[3], choices=range(1,5), metavar='categories_depth', type=int) | 38 parser.add_argument('--categories_depth', dest='categories_depth', action='store', nargs=1, default=[3], choices=range(1,5), metavar='categories_depth', type=int) |
| 39 parser.add_argument('--plot_format', dest='plot_format', action='store', nargs=1, choices=['pdf', 'png', 'svg'], metavar='plot_format', type=str) | 39 parser.add_argument('--plot_format', dest='plot_format', action='store', nargs=1, choices=['pdf', 'png', 'svg'], metavar='plot_format', type=str) |
| 40 parser.add_argument('--threshold', dest='threshold', action='store', nargs=2, metavar=('yMin', 'yMax'), type=float) | 40 parser.add_argument('--threshold', dest='threshold', action='store', nargs=2, metavar=('yMin', 'yMax'), type=float) |
| 41 #Internal variables | 41 #Internal variables |
| 42 parser.add_argument('--log_report', dest='log_report', action='store', nargs=1, metavar='log_filename', type=str) | 42 parser.add_argument('--log_report', dest='log_report', action='store', nargs=1, metavar='log_filename', type=str) |
| 43 parser.add_argument('--galaxy_root', dest='GALAXY_ROOT_DIR', action='store', nargs=1, metavar='galaxy_root_path', type=str) | |
| 44 parser.add_argument('--tool_dir', dest='GALAXY_TOOL_DIR', action='store', nargs=1, metavar='galaxy_tool_dir_path', type=str) | 43 parser.add_argument('--tool_dir', dest='GALAXY_TOOL_DIR', action='store', nargs=1, metavar='galaxy_tool_dir_path', type=str) |
| 45 args = parser.parse_args() | 44 args = parser.parse_args() |
| 46 return args | 45 return args |
| 47 | |
| 48 def make_tmp_dir(galaxy_root): | |
| 49 parent_dir = os.path.join(galaxy_root, 'database/tmp/') | |
| 50 if os.path.exists(parent_dir): | |
| 51 tmp_dir = tempfile.mkdtemp(prefix='tmp', suffix='', dir=parent_dir) | |
| 52 else: | |
| 53 tmp_dir = tempfile.mkdtemp(prefix='tmp', suffix='', dir='.') | |
| 54 return tmp_dir | |
| 55 | 46 |
| 56 def mv_and_rename_user_indexes(stranded_index, unstranded_index): | 47 def mv_and_rename_user_indexes(stranded_index, unstranded_index): |
| 57 index='index' | 48 index='index' |
| 58 shutil.copy(stranded_index, index + '.stranded.index') | 49 shutil.copy(stranded_index, index + '.stranded.index') |
| 59 shutil.copy(unstranded_index, index + '.unstranded.index') | 50 shutil.copy(unstranded_index, index + '.unstranded.index') |
| 107 args = get_arg() | 98 args = get_arg() |
| 108 | 99 |
| 109 if not (args.output_pdf or args.output_png or args.output_svg or args.output_indexes or args.output_count): | 100 if not (args.output_pdf or args.output_png or args.output_svg or args.output_indexes or args.output_count): |
| 110 exit_and_explain('Error: no output to return\nProcess Aborted\n') | 101 exit_and_explain('Error: no output to return\nProcess Aborted\n') |
| 111 | 102 |
| 112 tmp_dir = make_tmp_dir(args.GALAXY_TOOL_DIR[0]) | 103 tmp_dir = tempfile.mkdtemp(prefix='tmp', suffix='') |
| 113 os.chdir(tmp_dir) | |
| 114 | 104 |
| 115 logging.basicConfig(level=logging.INFO, filename=args.log_report[0], filemode="a+", format='%(message)s') | 105 logging.basicConfig(level=logging.INFO, filename=args.log_report[0], filemode="a+", format='%(message)s') |
| 116 | 106 |
| 117 alfa_path = os.path.join(args.GALAXY_TOOL_DIR[0], 'ALFA.py') | 107 alfa_path = os.path.join(args.GALAXY_TOOL_DIR[0], 'ALFA.py') |
| 118 | 108 |