.. _`bio/snp-mutator`:

SNP-MUTATOR
===========


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

Generate mutated sequence files from a reference genome.


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    NUM_SIMULATIONS = 2

    rule snpmutator:
        input:
            "{sample}.fa"
        output:
            vcf = "{sample}.mutated.vcf",
            sequences = expand(
                "{{sample}}_mutated_{simulation_number}.fasta",
                simulation_number=range(1, NUM_SIMULATIONS + 1)
            )
        params:
            num_simulations = NUM_SIMULATIONS,
            extra = " ".join([
                "--num-substitutions 2",
                "--num-insertions 2",
                "--num-deletions 0"
            ]),
        log:
            "logs/snp-mutator/test/{sample}.log"
        wrapper:
            "v3.0.1/bio/snp-mutator"

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.


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

* ``snp-mutator=1.2.0``




Authors
-------

* Michael Hall


Code
----

.. code-block:: python

    """Snakemake wrapper for SNP Mutator."""

    __author__ = "Michael Hall"
    __copyright__ = "Copyright 2019, Michael Hall"
    __email__ = "mbhall88@gmail.com"
    __license__ = "MIT"


    from snakemake.shell import shell
    from pathlib import Path

    # Placeholder for optional parameters
    extra = snakemake.params.get("extra", "")
    num_simulations = snakemake.params.get("num_simulations", 100)
    fasta_outdir = Path(snakemake.output.sequences[0]).absolute().parent
    # Formats the log redrection string
    log = snakemake.log_fmt_shell(stdout=True, stderr=True)

    # Executed shell command
    shell(
        "snpmutator {extra} "
        "--num-simulations {num_simulations} "
        "--vcf {snakemake.output.vcf} "
        "-F {fasta_outdir} "
        "{snakemake.input} {log} "
    )


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