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Merge pull request #102 from Ecogenomics/master
Merge master branch for release 0.2.1
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,3 @@ | ||
| global-exclude config.py | ||
| global-include pfam_search.pl | ||
| global-include *.pm | ||
| include genome_1.fna genome_2.fna genome_3.fna | ||
| global-exclude genome_*_protein.fna | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,103 @@ | ||
| ############################################################################### | ||
| # # | ||
| # This program is free software: you can redistribute it and/or modify # | ||
| # it under the terms of the GNU General Public License as published by # | ||
| # the Free Software Foundation, either version 3 of the License, or # | ||
| # (at your option) any later version. # | ||
| # # | ||
| # This program is distributed in the hope that it will be useful, # | ||
| # but WITHOUT ANY WARRANTY; without even the implied warranty of # | ||
| # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # | ||
| # GNU General Public License for more details. # | ||
| # # | ||
| # You should have received a copy of the GNU General Public License # | ||
| # along with this program. If not, see <http://www.gnu.org/licenses/>. # | ||
| # # | ||
| ############################################################################### | ||
|
|
||
| __author__ = 'Donovan Parks' | ||
| __copyright__ = 'Copyright 2014' | ||
| __credits__ = ['Donovan Parks'] | ||
| __license__ = 'GPL3' | ||
| __maintainer__ = 'Donovan Parks' | ||
| __email__ = 'donovan.parks@gmail.com' | ||
|
|
||
| import os | ||
| import errno | ||
| import sys | ||
| import logging | ||
| import ntpath | ||
| import re | ||
| import gzip | ||
|
|
||
|
|
||
| def is_float(s): | ||
| """Check if a string can be converted to a float. | ||
| Parameters | ||
| ---------- | ||
| s : str | ||
| String to evaluate. | ||
| Returns | ||
| ------- | ||
| boolean | ||
| True if string can be converted, else False. | ||
| """ | ||
|
|
||
| try: | ||
| float(s) | ||
| except ValueError: | ||
| return False | ||
|
|
||
| return True | ||
|
|
||
|
|
||
| def check_file_exists(input_file): | ||
| """Check if file exists.""" | ||
| if not os.path.exists(input_file) or not os.path.isfile(input_file): | ||
| logger = logging.getLogger('timestamp') | ||
| logger.error('Input file does not exists: ' + input_file + '\n') | ||
| sys.exit() | ||
|
|
||
|
|
||
| def check_dir_exists(input_dir): | ||
| """Check if directory exists.""" | ||
| if not os.path.exists(input_dir) or not os.path.isdir(input_dir): | ||
| logger = logging.getLogger('timestamp') | ||
| logger.error('Input directory does not exists: ' + input_dir + '\n') | ||
| sys.exit() | ||
|
|
||
|
|
||
| def make_sure_path_exists(path): | ||
| """Create directory if it does not exist.""" | ||
|
|
||
| if not path: | ||
| # lack of a path qualifier is acceptable as this | ||
| # simply specifies the current directory | ||
| return | ||
|
|
||
| try: | ||
| os.makedirs(path) | ||
| except OSError as exception: | ||
| if exception.errno != errno.EEXIST: | ||
| logger = logging.getLogger('timestamp') | ||
| logger.error('Specified path could not be created: ' + path + '\n') | ||
| sys.exit() | ||
|
|
||
|
|
||
| def remove_extension(filename, extension=None): | ||
| """Remove extension from filename. | ||
| A specific extension can be specified, otherwise | ||
| the extension is taken as all characters after the | ||
| last period. | ||
| """ | ||
| f = ntpath.basename(filename) | ||
|
|
||
| if extension and f.endswith(extension): | ||
| f = f[0:f.rfind(extension)] | ||
| else: | ||
| f = os.path.splitext(f)[0] | ||
|
|
||
| if f[-1] == '.': | ||
| f = f[0:-1] | ||
|
|
||
| return f |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,102 @@ | ||
| ############################################################################### | ||
| # # | ||
| # This program is free software: you can redistribute it and/or modify # | ||
| # it under the terms of the GNU General Public License as published by # | ||
| # the Free Software Foundation, either version 3 of the License, or # | ||
| # (at your option) any later version. # | ||
| # # | ||
| # This program is distributed in the hope that it will be useful, # | ||
| # but WITHOUT ANY WARRANTY; without even the implied warranty of # | ||
| # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # | ||
| # GNU General Public License for more details. # | ||
| # # | ||
| # You should have received a copy of the GNU General Public License # | ||
| # along with this program. If not, see <http://www.gnu.org/licenses/>. # | ||
| # # | ||
| ############################################################################### | ||
|
|
||
| __author__ = 'Donovan Parks' | ||
| __copyright__ = 'Copyright 2014' | ||
| __credits__ = ['Donovan Parks', 'Connor Skennerton'] | ||
| __license__ = 'GPL3' | ||
| __maintainer__ = 'Donovan Parks' | ||
| __email__ = 'donovan.parks@gmail.com' | ||
|
|
||
| import os | ||
| import types | ||
| import tempfile | ||
| import argparse | ||
|
|
||
|
|
||
| class ChangeTempAction(argparse.Action): | ||
| """Action for changing the directory used for temporary files. | ||
| Example: | ||
| <parse>.add_argument('--tmpdir', action=ChangeTempAction, default=tempfile.gettempdir(), help="specify alternative directory for temporary files") | ||
| """ | ||
|
|
||
| def __call__(self, parser, namespace, values, option_string=None): | ||
| if os.path.isdir(values): | ||
| tempfile.tempdir = values | ||
| setattr(namespace, self.dest, values) | ||
| else: | ||
| raise argparse.ArgumentTypeError( | ||
| 'The value of %s must be a valid directory' % option_string) | ||
|
|
||
|
|
||
| class CustomHelpFormatter(argparse.HelpFormatter): | ||
| """Provide a customized format for help output. | ||
| http://stackoverflow.com/questions/9642692/argparse-help-without-duplicate-allcaps | ||
| """ | ||
|
|
||
| def _get_help_string(self, action): | ||
| """Place default value in help string.""" | ||
| h = action.help | ||
| if '%(default)' not in action.help: | ||
| if action.default != '' and action.default != [] and action.default is not None and type(action.default) != types.BooleanType: | ||
| if action.default is not argparse.SUPPRESS: | ||
| defaulting_nargs = [ | ||
| argparse.OPTIONAL, argparse.ZERO_OR_MORE] | ||
|
|
||
| if action.option_strings or action.nargs in defaulting_nargs: | ||
| if '\n' in h: | ||
| lines = h.splitlines() | ||
| lines[0] += ' (default: %(default)s)' | ||
| h = '\n'.join(lines) | ||
| else: | ||
| h += ' (default: %(default)s)' | ||
| return h | ||
|
|
||
| def _format_action_invocation(self, action): | ||
| """Removes duplicate ALLCAPS with positional arguments.""" | ||
| if not action.option_strings: | ||
| default = self._get_default_metavar_for_positional(action) | ||
| metavar, = self._metavar_formatter(action, default)(1) | ||
| return metavar | ||
|
|
||
| else: | ||
| parts = [] | ||
|
|
||
| # if the Optional doesn't take a value, format is: | ||
| # -s, --long | ||
| if action.nargs == 0: | ||
| parts.extend(action.option_strings) | ||
|
|
||
| # if the Optional takes a value, format is: | ||
| # -s ARGS, --long ARGS | ||
| else: | ||
| default = self._get_default_metavar_for_optional(action) | ||
| args_string = self._format_args(action, default) | ||
| for option_string in action.option_strings: | ||
| parts.append(option_string) | ||
|
|
||
| return '%s %s' % (', '.join(parts), args_string) | ||
|
|
||
| return ', '.join(parts) | ||
|
|
||
| def _get_default_metavar_for_optional(self, action): | ||
| return action.dest.upper() | ||
|
|
||
| def _get_default_metavar_for_positional(self, action): | ||
| return action.dest |
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