Scripts error when called with -h option during option parsing

[adamrp]

E.g., if you have in your qiime_config file:

assign_taxonomy_reference_seqs_fp some/nonexistent/file.txt

and then call assign_taxonomy.py -h (or --help), you will get this error:

Traceback (most recent call last): File "/Users/adro2179/git_repos/qiime/scripts/assign_taxonomy.py", line 305, in main() File "/Users/adro2179/git_repos/qiime/scripts/assign_taxonomy.py", line 157, in main option_parser, opts, args = parse_command_line_parameters(**script_info) File "/Users/adro2179/git_repos/pycogent/cogent/util/option_parsing.py", line 243, in parse_command_line_parameters opts,args = parser.parse_args(command_line_args) File "/Users/adro2179/bin/python-2.7.1-release/lib/python2.7/optparse.py", line 1378, in parse_args values = self.get_default_values() File "/Users/adro2179/bin/python-2.7.1-release/lib/python2.7/optparse.py", line 1323, in get_default_values defaults[option.dest] = option.check_value(opt_str, default) File "/Users/adro2179/bin/python-2.7.1-release/lib/python2.7/optparse.py", line 769, in check_value return checker(self, opt, value) File "/Users/adro2179/git_repos/pycogent/cogent/util/option_parsing.py", line 31, in check_existing_filepath "option %s: file does not exist: %r" % (opt, value)) optparse.OptionValueError: option --id_to_taxonomy_fp: file does not exist: 'some/nonexistent/file.txt'

Whereas executing assign_taxonomy.py without _any_options kind of works, but does not print the various options.

In my opinion, the -h option should categorically not raise errors.

[gregcaporaso]

Good catch. This is a little tricky to handle, but the way to do it would be to modify line 78 of Qiime/scripts/assign_taxonomy.py to something like:

qiime_config_reference_seqs_fp = qiime_config['assign_taxonomy_reference_seqs_fp']
if os.path.exists(qiime_config_reference_seqs_fp):
    default_reference_seqs_fp = qiime_config_reference_seqs_fp
else:
    default_reference_seqs_fp = None

The issue with this is that it will be confusing if you don't know that the assign_taxonomy_reference_seqs_fp in your qiime_config is bad, but I guess the solution to that is that you run print_qiime_config.py -t.