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.. _make_otu_table:
.. index:: make_otu_table.py
*make_otu_table.py* -- Make OTU table
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
**Description:**
The script `make_otu_table.py <./make_otu_table.html>`_ tabulates the number of times an OTU is found in each sample, and adds the taxonomic predictions for each OTU in the last column if a taxonomy file is supplied.
**Usage:** :file:`make_otu_table.py [options]`
**Input Arguments:**
.. note::
**[REQUIRED]**
-i, `-`-otu_map_fp
Path to the input OTU map (i.e., the output from `pick_otus.py <./pick_otus.html>`_)
**[OPTIONAL]**
-t, `-`-taxonomy
Path to taxonomy assignment, containing the assignments of \ taxons to sequences (i.e., resulting txt file from `assign_taxonomy.py <./assign_taxonomy.html>`_) [default: None]
-o, `-`-output_fp
The output filepath
-e, `-`-exclude_otus_fp
Path to a file listing OTU identifiers that should not be included in the OTU table (e.g., the output of `identify_chimeric_seqs.py <./identify_chimeric_seqs.html>`_) or a fasta file where seq ids should be excluded (e.g., failures fasta file from `align_seqs.py <./align_seqs.html>`_)
**Output:**
The output of `make_otu_table.py <./make_otu_table.html>`_ is a tab-delimited text file, where the columns correspond to Samples and rows correspond to OTUs and the number of times a sample appears in a particular OTU.
Make an OTU table from an OTU map (i.e., result from `pick_otus.py <./pick_otus.html>`_) and a taxonomy assignment file (i.e., result from `assign_taxonomy.py <./assign_taxonomy.html>`_). Write the output file to otu_table.txt.
::
make_otu_table.py -i otu_map.txt -t tax_assignments.txt -o otu_table.txt
Make an OTU table, excluding the sequences listed in chimeric_seqs.txt
::
make_otu_table.py -i otu_map.txt -o otu_table.txt -e chimeric_seqs.txt
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