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.. _pick_otus_through_otu_table:
.. index:: pick_otus_through_otu_table.py
*pick_otus_through_otu_table.py* -- A workflow script for picking OTUs through building OTU tables
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
**Description:**
This script takes a sequence file and performs all processing steps through building the OTU table.
**Usage:** :file:`pick_otus_through_otu_table.py [options]`
**Input Arguments:**
.. note::
**[REQUIRED]**
-i, `-`-input_fp
The input fasta 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]
-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]
-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:**
This script will produce an OTU mapping file (`pick_otus.py <./pick_otus.html>`_), a representative set of sequences (FASTA file from `pick_rep_set.py <./pick_rep_set.html>`_), a sequence alignment file (FASTA file from `align_seqs.py <./align_seqs.html>`_), taxonomy assignment file (from `assign_taxonomy.py <./assign_taxonomy.html>`_), a filtered sequence alignment (from `filter_alignment.py <./filter_alignment.html>`_), a phylogenetic tree (Newick file from `make_phylogeny.py <./make_phylogeny.html>`_) and an OTU table (from `make_otu_table.py <./make_otu_table.html>`_).
**Simple example:**
The following command will start an analysis on inseq1.fasta (-i), which is a post-split_libraries fasta file. The sequence identifiers in this file should be of the form <sample_id>_<unique_seq_id>. The following steps, corresponding to the preliminary data preparation, are applied.
1. Pick OTUs with uclust at similarity of 0.97;
2. Pick a representative set with the most_abundant method;
3. Align the representative set with PyNAST;
4. Assign taxonomy with RDP classifier;
5. Filter the alignment prior to tree building - remove positions which are all gaps, and specified as 0 in the lanemask;
6. Build a phylogenetic tree with FastTree;
7. Build an OTU table.
All output files will be written to the directory specified by -o, and
subdirectories as appropriate.
::
pick_otus_through_otu_table.py -i inseqs1.fasta -o wf1/ -p custom_parameters.txt
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