Yes, we want it to be there (note that when reference based OTU picking is
used, it is set to "" so there won't be a prefix, and if new clusters are
allowed (ref + denovo) we want the de novo clusters to not just be numbers,
so there isn't confusion or errors when matching these up to reference
database.



On Tue, Apr 9, 2013 at 12:42 PM, Greg Caporaso <notifications@github.com>wrote:

> In qiime/pick_otus.py:
>
> > +         'suppress_new_clusters':False
> > +         }
> > +
> > +
> > +        _params.update(params)
> > +        OtuPicker.__init__(self, _params)
> > +
> > +    def __call__(self,
> > +                 seq_path,
> > +                 refseqs_fp,
> > +                 output_dir='.',
> > +                 log_path=None,
> > +                 HALT_EXEC=False,
> > +                 result_path=None,
> > +                 failure_path=None,
> > +                 otu_prefix="denovo"):
>
> is otu_prefix relevant here? It seems like we don't need that since the
> OTU ids will be the reference sequence ids, but if we do want to include it
> it should probably be reference by default.
>
> —
> Reply to this email directly or view it on GitHub<https://github.com/qiime/qiime/pull/844/files#r3719680>
> .
>