compute_taxonomy_ratios.py – Compute the log ratio abundance of specified taxonomic groups.

Description:

Compute the log ratio abundance of specified taxonomic groups. This method is based on the microbial dysbiosis index described in Gevers et al. 2014: http://www.ncbi.nlm.nih.gov/pubmed/24629344

Usage: compute_taxonomy_ratios.py [options]

Input Arguments:

Note

[OPTIONAL]

-i, --input

The input BIOM table [REQUIRED if not passing -s]

-o, --output

Path to where the output will be written; this will be a new sample metadata mapping file [REQUIRED if not passing -s]

--increased

Comma-separated list of taxa whose abundances are included in the numerator of the ratio [REQUIRED if not passing -s or -e]

--decreased

Comma-separated list of taxa whose abundances are included in the denominator of the ratio [REQUIRED if not passing -s or -e]

-e, --index

Apply an existing index. Options are: md [REQUIRED if not passing -s or –increased and –decreased]

-n, --name

Column name for the index in the output file [default: ‘index’, or value passed as -e if provided]

-m, --mapping_file

A mapping file containing data that should be included in the output file [default: no additional mapping file data is included in output]

-k, --key

Metadata key to use for computing index [default: taxonomy]

-s, --show_indices

List known indices and exit [default: False]

Output:

By default, a minimal QIIME mapping file is created containing two columns: SampleID and the index. If -m is provided, the information in that mapping file is merged into the default output mapping file.

Example:

Compute the microbial dysbiosis (MD) index

compute_taxonomy_ratios.py -i table.biom.gz -e md -o md.txt

Example:

Compute the microbial dysbiosis (MD) index and add it to an existing mapping file

compute_taxonomy_ratios.py -i table.biom.gz -e md -o map_w_md.txt -m map.txt

Example:

Compute the log of the abundance of p__Firmicutes plus p__Fusobacteria divided by the abundance of p__Bacteroidetes and write the results to custom_index.txt.

compute_taxonomy_ratios.py -i table.biom.gz --increased p__Firmicutes,p__Fusobacteria --decreased p__Bacteroidetes -o custom_index.txt