.. _`bio/rasusa`:

RASUSA
======


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

Randomly subsample sequencing reads to a specified coverage.

**URL**: https://github.com/mbhall88/rasusa

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule subsample:
        input:
            r1="{sample}.r1.fq",
            r2="{sample}.r2.fq",
        output:
            r1="{sample}.subsampled.r1.fq",
            r2="{sample}.subsampled.r2.fq",
        params:
            options="--seed 15",
            genome_size="3mb",  # required, unless `bases` is given
            coverage=20,  # required, unless `bases is given
            #bases="2gb"
        log:
            "logs/subsample/{sample}.log",
        wrapper:
            "v3.0.1/bio/rasusa"

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
---------------------

* ``rasusa=0.7.1``

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

* Reads to subsample in FASTA/Q format. Input files can be named or unnamed.

**Output:**

* File paths to write subsampled reads to. If using paired-end data, make sure there are two output files in the same order as the input.



Params
------

* ``bases``: Explicitly set the number of bases required e.g., 4.3kb, 7Tb, 9000, 4.1MB |nl| If this option is given, ``coverage`` and ``genome_size`` are ignored


* ``coverage``: The desired coverage to sub-sample the reads to. |nl| If ``bases`` is not provided, this option and ``genome_size`` are required


* ``genome_size``: Genome size to calculate coverage with respect to. e.g., 4.3kb, 7Tb, 9000, 4.1MB |nl| Alternatively, a FASTA/Q index file can be provided and the genome size will be set to the sum of all reference sequences. |nl| If ``bases`` is not provided, this option and ``coverage`` are required


* ``options``: Any other options as listed in `the docs <https://github.com/mbhall88/rasusa#usage>`_.





Authors
-------

* Michael Hall


Code
----

.. code-block:: python

    __author__ = "Michael Hall"
    __copyright__ = "Copyright 2020, Michael Hall"
    __email__ = "michael@mbh.sh"
    __license__ = "MIT"


    from snakemake.shell import shell


    options = snakemake.params.get("options", "")

    bases = snakemake.params.get("bases")
    if bases is not None:
        options += " -b {}".format(bases)
    else:
        covg = snakemake.params.get("coverage")
        gsize = snakemake.params.get("genome_size")
        if covg is None or gsize is None:
            raise ValueError(
                "If `bases` is not given, then `coverage` and `genome_size` must be"
            )
        options += " -g {gsize} -c {covg}".format(gsize=gsize, covg=covg)

    shell("rasusa {options} -i {snakemake.input} -o {snakemake.output} 2> {snakemake.log}")


.. |nl| raw:: html

   <br>