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.. _truncate_reverse_primer:
.. index:: truncate_reverse_primer.py
*truncate_reverse_primer.py* -- Takes a demultiplexed fasta file, finds a specified reverse primer sequence, and truncates this primer and subsequent sequences following the reverse primer.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
**Description:**
Takes input mapping file and fasta sequences which have already have been demultiplexed (via `split_libraries.py <./split_libraries.html>`_, `denoise_wrapper.py <./denoise_wrapper.html>`_, `ampliconnoise.py <./ampliconnoise.html>`_, etc.) with fasta labels that are in QIIME format, i.e., SampleID_#. This script will use the SampleID and a mapping file with a ReversePrimer column to find the reverse primer by local alignment and remove this and any subsequent sequence in a filtered output fasta file.
**Usage:** :file:`truncate_reverse_primer.py [options]`
**Input Arguments:**
.. note::
**[REQUIRED]**
-f, `-`-fasta_fp
Fasta file. Needs to have fasta labels in proper demultiplexed format.
-m, `-`-mapping_fp
Mapping filepath. ReversePrimer field required. Reverse primers need to be in 5'->3' orientation.
**[OPTIONAL]**
-o, `-`-output_dir
Output directory. Will be created if does not exist. [default: .]
-z, `-`-truncate_option
Truncation option. The default option, "truncate_only" will try to find the reverse primer to truncate, and if not found, will write the sequence unchanged. If set to "truncate_remove", sequences where the reverse primer is not found will not be written. [default: truncate_only]
-M, `-`-primer_mismatches
Number of mismatches allowed in the reverse primer. [default: 2]
**Output:**
Truncated version of the input fasta file (based on input name with 'seqs_rev_primer_truncated' appended) will be generated in the output directory, along with a .log file.
**Example:**
Find, truncate reverse primers from the fasta file seqs.fna, with the SampleIDs and reverse primers specified in Mapping_File_Rev_Primer.txt, writes output fasta file to the reverse_primer_removed directory:
::
truncate_reverse_primer.py -f seqs.fna -m Mapping_File_Rev_Primer.txt -o reverse_primer_removed/
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