Wouldn't it be important to tell the user which samples are being ignored, just in case they assume they are in there? say in a log file or verbose output?
On Feb 20, 2013, at 3:25 PM, Greg Caporaso <notifications@github.com> wrote:

> In doc/developer/coding_guidelines.rst:
> 
> >  
> >   * if you have been passing dest= to parser.add_option, note that you do not need to do this -- dest will be generated from the long format option (e.g., the value passed to --input_file will be stored in input_file)
> >   
> >   * Your usage string should be defined in a variable called ``usage_str`` as a multiline string outside of the function that is using it. This makes the code look neater, and will help automated documentation tools find that text (eventually). 
> >  
> > + * Scripts that process a metadata mapping file and a data file (biom-formatted otu table, distance matrix, principal coordinates file, etc.) within QIIME, should execute faultlessly in the case where sample identifiers exist only in the mapping file but not in the data files.
> For clarity, this would be better:
> 
> 
> Scripts that process a metadata mapping file and a data file (biom-formatted otu table, distance matrix, principal coordinates file, etc.) within QIIME, should always ignore sample identifiers that exist in the mapping file, but not in the data file.
> 
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