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.. _inflate_denoiser_output:
.. index:: inflate_denoiser_output.py
*inflate_denoiser_output.py* -- Inflate denoiser results so they can be passed directly to OTU pickers.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
**Description:**
Inflate denoiser results so they can be passed directly to `pick_otus.py <./pick_otus.html>`_, `parallel_pick_otus_uclust_ref.py <./parallel_pick_otus_uclust_ref.html>`_, or `pick_de_novo_otus.py <./pick_de_novo_otus.html>`_. Note that the results of this script have not be abundance sorted, so they must be before being passed to the OTU picker. The uclust OTU pickers incorporate this abundance presorting by default.
The inflation process writes each centroid sequence n times, where n is the number of reads that cluster to that centroid, and writes each singleton once. Flowgram identifiers are mapped back to post-split_libraries identifiers in this process (i.e., identifiers in fasta fps).
**Usage:** :file:`inflate_denoiser_output.py [options]`
**Input Arguments:**
.. note::
**[REQUIRED]**
-c, `-`-centroid_fps
The centroid fasta filepaths
-s, `-`-singleton_fps
The singleton fasta filepaths
-f, `-`-fasta_fps
The input (to denoiser) fasta filepaths
-d, `-`-denoiser_map_fps
The denoiser map filepaths
-o, `-`-output_fasta_fp
The output fasta filepath
**Output:**
Inflate the results of a single denoiser run.
::
inflate_denoiser_output.py -c centroids.fasta -s singletons.fasta -f seqs.fna -d denoiser_mapping.txt -o inflated_seqs.fna
Inflate the results of multiple denoiser runs to a single inflated_seqs.fna file.
::
inflate_denoiser_output.py -c centroids1.fasta,centroids2.fasta -s singletons1.fasta,singletons2.fasta -f seqs1.fna,seqs2.fna -d denoiser_mapping1.txt,denoiser_mapping2.txt -o inflated_seqs_combined.fna
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