.. _`bio/meryl/sets`:

MERYL SETS
==========


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

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_union:
        input:
            "{genome}",
            "{genome}",
        output:
            directory("{genome}_union/"),
        log:
            "logs/{genome}.union.log",
        params:
            command="union-sum",
        wrapper:
            "v3.0.4/bio/meryl/sets"


    rule meryl_intersect:
        input:
            "{genome}",
            "{genome}",
        output:
            directory("{genome}_intersect/"),
        log:
            "logs/{genome}.intersect.log",
        params:
            command="intersect-max",
        wrapper:
            "v3.0.4/bio/meryl/sets"


    rule meryl_subtract:
        input:
            "{genome}",
            "{genome}",
        output:
            directory("{genome}_subtract/"),
        log:
            "logs/{genome}.subtract.log",
        params:
            command="subtract",
        wrapper:
            "v3.0.4/bio/meryl/sets"


    rule meryl_difference:
        input:
            "{genome}",
            "{genome}",
        output:
            directory("{genome}_difference/"),
        log:
            "logs/{genome}.difference.log",
        params:
            command="difference",
        wrapper:
            "v3.0.4/bio/meryl/sets"

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 how to handle the kmer sets: `union` (number of inputs) [default], `union-min` (union with minimum count), `union-max` (union with maximum count), `union-sum` (union with sum of the counts), `intersect` (intersect with counts in the first input), `intersect-min` (intersect with minimum count), `intersect-max` (intersect with maximum count), `intersect-sum` (intersect with sum of counts), `subtract` (counts from first input, subtracting counts from the other inputs), `difference` (counts from first input, but none of the other inputs), or `symmetric-difference` (exactly one input).


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

* ``meryl=2013``

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

* meryl database(s)

**Output:**

* meryl database




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=True, stderr=True)


    command = snakemake.params.get("command", "union")
    assert command in [
        "union",
        "union-min",
        "union-max",
        "union-sum",
        "intersect",
        "intersect-min",
        "intersect-max",
        "intersect-sum",
        "subtract",
        "difference",
        "symmetric-difference",
    ], "invalid command specified."


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


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