.. _`bio/meryl/stats`:

MERYL STATS
===========


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

A genomic k-mer counter (and sequence utility) with nice features.


**URL**: https://github.com/marbl/meryl

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule meryl_stats:
        input:
            "{genome}",
        output:
            "{genome}.stats",
        log:
            "logs/meryl_stats/{genome}.log",
        params:
            command="statistics",
        wrapper:
            "v3.0.4/bio/meryl/stats"

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
-----

* The `command` param allows to specify which stats to print: `statistics` (display total, unique, distinct kmers) [default], `histogram` (display kmer frequency), or `print` (display kmers).


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

* ``meryl=2013``

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

* meryl database(s)

**Output:**

* meryl stats (either the kmers, statistics, or histogram)




Authors
-------

* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Filipe G. Vieira"
    __copyright__ = "Copyright 2022, Filipe G. Vieira"
    __license__ = "MIT"


    from snakemake.shell import shell


    log = snakemake.log_fmt_shell(stdout=False, stderr=True)


    command = snakemake.params.get("command", "statistics")
    assert command in [
        "statistics",
        "histogram",
        "print",
    ], "invalid command specified."


    shell("meryl {command} {snakemake.input} > {snakemake.output} {log}")


.. |nl| raw:: html

   <br>