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