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? 
I just thought it would be convenient because the data would be readily
available for Emperor or Pandas. This way you could easily do some
fine-grained statistical analysis using the data in your mapping file
and this index. If others can comment on this that would be great!

On (Dec-08-14|12:55), Daniel McDonald wrote:
> > +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."""
> 
> 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>.
> >
> 
> ---
> Reply to this email directly or view it on GitHub:
> https://github.com/biocore/qiime/pull/1760/files#r21484587