alpha_rarefaction.py – A workflow script for performing alpha rarefaction

Description:

The steps performed by this script are: Generate rarefied OTU tables; compute alpha diversity metrics for each rarefied OTU table; collate alpha diversity results; and 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: 2]

--retain_intermediate_files

Retain intermediate files: rarefied OTU tables (rarefaction) and alpha diversity results (alpha_div). By default these will be erased [default: False]

Output:

The primary interface for the results will be OUTPUT_DIR/alpha_rarefaction_plots/rarefaction_plots.html where OUTPUT_DIR is the value you specify with -o. You can open this in a web browser for interactive alpha rarefaction plots.

Example:

Given an OTU table, a phylogenetic tree, a mapping file, and a max sample depth, compute alpha rarefaction plots for the PD, observed species and chao1 metrics. To specify alternative metrics pass a parameter file via -p. We generally recommend that the max depth specified here (-e) is the same as the even sampling depth provided to beta_diversity_through_plots (also -e).

alpha_rarefaction.py -i otu_table.biom -o arare_max100/ -t rep_set.tre -m Fasting_Map.txt -e 100