.. _`bio/bedtools/complement`:

COMPLEMENTBED
=============


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

Maps all regions of the genome which are not covered by the input.


**URL**: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule bedtools_complement_bed:
        input:
            in_file="a.bed",
            genome="dummy.genome"
        output:
            "results/bed-complement/a.complement.bed"
        params:
            ## Add optional parameters
            extra="-L"
        log:
            "logs/a.complement.bed.log"
        wrapper:
            "v4.6.0-24-g250dd3e/bio/bedtools/complement"

    rule bedtools_complement_vcf:
        input:
            in_file="a.vcf",
            genome="dummy.genome"
        output:
            "results/vcf-complement/a.complement.vcf"
        params:
            ## Add optional parameters
            extra="-L"
        log:
            "logs/a.complement.vcf.log"
        wrapper:
            "v4.6.0-24-g250dd3e/bio/bedtools/complement"

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
-----

* This program/wrapper does not handle multi-threading.

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

* ``bedtools=2.31.1``

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

* ``in_file``: interval files (BED/GFF/VCF)
* ``genome``: genome file

**Output:**

* complemented BED/GFF/VCF file



Params
------

* ``extra``: additional program arguments (except `-i` and `-g`)




Authors
-------

* Antonie Vietor


Code
----

.. code-block:: python

    __author__ = "Antonie Vietor"
    __copyright__ = "Copyright 2020, Antonie Vietor"
    __email__ = "antonie.v@gmx.de"
    __license__ = "MIT"

    from snakemake.shell import shell

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

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

    shell(
        "(bedtools complement"
        " {extra}"
        " -i {snakemake.input.in_file}"
        " -g {snakemake.input.genome}"
        " > {snakemake.output[0]})"
        " {log}"
    )


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