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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]
-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

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