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.. _alpha_rarefaction:
.. index:: alpha_rarefaction.py
*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:** :file:`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
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