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.. _parallel_alpha_diversity:
.. index:: parallel_alpha_diversity.py
*parallel_alpha_diversity.py* -- Parallel alpha diversity
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
**Description:**
This script performs like the `alpha_diversity.py <./alpha_diversity.html>`_ script, but is intended to make use of multicore/multiprocessor environments to perform analyses in parallel.
**Usage:** :file:`parallel_alpha_diversity.py [options]`
**Input Arguments:**
.. note::
**[REQUIRED]**
-i, `-`-input_path
Input path, must be directory [REQUIRED]
-o, `-`-output_path
Output path, must be directory [REQUIRED]
**[OPTIONAL]**
-t, `-`-tree_path
Path to newick tree file, required for phylogenetic metrics [default: None]
-N, `-`-alpha_diversity_fp
Full path to scripts/`alpha_diversity.py <./alpha_diversity.html>`_ [default: /Users/jistombaugh/Dropbox/Qiime_work/scripts/`alpha_diversity.py <./alpha_diversity.html>`_]
-m, `-`-metrics
Metrics to use, comma delimited
-P, `-`-poller_fp
Full path to qiime/parallel/`poller.py <./poller.html>`_ [default: /Users/jistombaugh/Dropbox/Qiime_work/scripts/`poller.py <./poller.html>`_]
-R, `-`-retain_temp_files
Retain temporary files after runs complete (useful for debugging) [default: False]
-S, `-`-suppress_submit_jobs
Only split input and write commands file - don't submit jobs [default: False]
-T, `-`-poll_directly
Poll directly for job completion rather than running poller as a separate job. If -T is specified this script will not return until all jobs have completed. [default: False]
-U, `-`-cluster_jobs_fp
Path to cluster jobs script (defined in qiime_config) [default: /Users/jistombaugh/Dropbox/Qiime_work/scripts/`start_parallel_jobs.py <./start_parallel_jobs.html>`_]
-W, `-`-suppress_polling
Suppress polling of jobs and merging of results upon completion [default: False]
-X, `-`-job_prefix
Job prefix [default: descriptive prefix + random chars]
-Y, `-`-python_exe_fp
Full path to python executable [default: /Library/Frameworks/Python.framework/Versions/2.7/bin/python]
-Z, `-`-seconds_to_sleep
Number of seconds to sleep between checks for run completion when polling runs [default: 60]
-O, `-`-jobs_to_start
Number of jobs to start [default: 1]
**Output:**
The resulting output will be the same number of files as supplied by the user. The resulting files are tab-delimited text files, where the columns correspond to alpha diversity metrics and the rows correspond to samples and their calculated diversity measurements.
**Example:**
Apply the observed_species, chao1, PD_whole_tree metrics (-m) to all otu tables in /home/qiime_user/rare/ (-i) and write the resulting output files to /home/qiime_user/out/ (-o, will be created if it doesn't exist). Use the tree file rep_set.tre (-t) when necessary.
::
parallel_alpha_diversity.py -i /home/qiime_user/rare/ -o /home/qiime_user/out -m observed_species,chao1,PD_whole_tree -t /home/qiime_user/rep_set.tre
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