Dysbiosis index

Addition of the microbial dysbiosis index described in [Gevers et al 2014](http://www.ncbi.nlm.nih.gov/pubmed/24629344). This method has been generalized to support other indices in the future as well.

@ElDeveloper, can you review please since you implemented the original approach? 
Depends what the user wants to do with it. This output can be used with
merge_mapping_files.py so if a user wants to merge it then it should be
pretty straight forward

On Mon, Dec 8, 2014 at 1:39 PM, Yoshiki Vázquez Baeza <
notifications@github.com> wrote:

> In scripts/compute_index.py:
>
> > +from biom import load_table
> > +
> > +from qiime.index import compute_index
> > +from qiime.util import parse_command_line_parameters, make_option
> > +
> > +
> > +script_info = {}
> > +script_info[
> > +    'brief_description'] = "Compute a taxonomy-based index"
> > +script_info[
> > +    'script_description'] = """Compute a taxonomy-based index to score each sample in a table. This method is based on the microbial dysbiosis index constructed in Gevers et al. 2014 (http://www.ncbi.nlm.nih.gov/pubmed/24629344)."""
> > +script_info[
> > +    'script_usage'] = [("Example:", "Compute the MD-index", """%prog -i $PWD/table.biom.gz -m md -o table.md.txt"""),
> > +                       ("Example:", "Compute an arbitrary index", """%prog -i $PWD/table.biom.gz --increased p__Firmicutes,p__Fusobacteria --decreased p__Bacteroidetes -o table.custom.txt""")]
> > +script_info[
> > +    'output_description'] = """Two columns, the first being the sample ID and the second being the index value for the sample."""
>
> Should the output be added to the mapping file instead?
>
> —
> Reply to this email directly or view it on GitHub
> <https://github.com/biocore/qiime/pull/1760/files#r21483314>.
>