.. _`bio/barrnap`:

BARRNAP
=======


.. image:: https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/barrnap?label=version%20update%20pull%20requests
   :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Abio/barrnap

BAsic Rapid Ribosomal RNA Predictor

**URL**: https://github.com/tseemann/barrnap

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule barrnap:
        input:
            fasta="{sample}.fasta",
        output:
            gff="{sample}.gff",
            fasta="{sample}_hits.fasta",
        params:
            kingdom="bac",
            extra="",
        threads: 1
        log:
            "logs/barrnap/{sample}.log",
        wrapper:
            "v3.0.1/bio/barrnap"

Note that input, output and log file paths can be chosen freely.

When running with

.. code-block:: bash

    snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.


Notes
-----

Multiple threads can be used during nhmmer search.

Software dependencies
---------------------

* ``barrnap=0.9``

Input/Output
------------
**Input:**

* ``fasta``: query fasta file

**Output:**

* ``gff``: The rRNA locations in GFF3 format.
* ``fasta``: Optional. Fasta file with the hit sequences.



Params
------

* ``extra``: additional parameters

* ``kingdom``: database to use, either Bacteria:`bac`, Archaea:`arc`, Eukaryota:`euk` or Metazoan Mitochondria:`mito`.




Authors
-------

* Curro Campuzano Jiménez


Code
----

.. code-block:: python

    """Snakemake wrapper for barrnap."""

    __author__ = "Curro Campuzano Jiménez"
    __copyright__ = "Copyright 2023, Curro Campuzano Jiménez"
    __email__ = "campuzanocurro@gmail.com"
    __license__ = "MIT"


    from snakemake.shell import shell

    log = snakemake.log_fmt_shell(stdout=False, stderr=True)
    extra = snakemake.params.get("extra", "")
    kingdom = snakemake.params.get("kingdom", "bac")

    fasta_out = snakemake.output.get("fasta")
    if fasta_out:
        extra += f" -o {fasta_out}"

    shell(
        "barrnap"
        " --threads {snakemake.threads}"
        " -k {kingdom}"
        " {extra}"
        " < {snakemake.input.fasta}"
        " > {snakemake.output.gff}"
        " {log}"
    )


.. |nl| raw:: html

   <br>