alpha_rarefaction.py – A workflow script for performing alpha rarefaction

Description:

The steps performed by this script are:

1. Generate rarefied OTU tables;
2. Compute alpha diversity metrics for each rarefied OTU table;
3. Collate alpha diversity results;
4. Generate alpha rarefaction plots.

Usage: alpha_rarefaction.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --otu_table_fp

The input otu table [REQUIRED]

-m, --mapping_fp

Path to the mapping file [REQUIRED]

-o, --output_dir

The output directory [REQUIRED]

[OPTIONAL]

-p, --parameter_fp

Path to the parameter file, which specifies changes to the default behavior. See http://www.qiime.org/documentation/file_formats.html#qiime-parameters . [if omitted, default values will be used]

-n, --num_steps

Number of steps (or rarefied OTU table sizes) to make between min and max counts [default: 10]

-f, --force

Force overwrite of existing output directory (note: existing files in output_dir will not be removed) [default: None]

-w, --print_only

Print the commands but don’t call them – useful for debugging [default: False]

-a, --parallel

Run in parallel where available [default: False]

-t, --tree_fp

Path to the tree file [default: None; REQUIRED for phylogenetic measures]

--min_rare_depth

The lower limit of rarefaction depths [default: 10]

-e, --max_rare_depth

The upper limit of rarefaction depths [default: median sequence/sample count]

-O, --jobs_to_start

Number of jobs to start. NOTE: you must also pass -a to run in parallel, this defines the number of jobs to be started if and only if -a is passed [default: 1]

Output:

The results of this script is a folder (“rare1/”) containing rarefied otu tables, alpha-diversity for each otu table, a file containing the results from collating the alpha-diversity results and a folder containing the rarefaction plots.

Example:

alpha_rarefaction.py -o rare1 -i otu_table.txt -t inseqs1_rep_set.tre -m inseqs1_mapping.txt -p custom_parameters.txt