.. _`bio/bedtools/intersect`:

INTERSECTBED
============


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

Intersect BED/BAM/VCF files with bedtools.

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

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule bedtools_merge:
        input:
            left="A.bed",
            right="B.bed"
        output:
            "A_B.intersected.bed"
        params:
            ## Add optional parameters
            extra="-wa -wb" ## In this example, we want to write original entries in A and B for each overlap.
        log:
            "logs/intersect/A_B.log"
        wrapper:
            "v3.0.1/bio/bedtools/intersect"

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

* ``bedtools=2.31.1``

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

* ``left``: Path to the left region file. Each feature in left region file is compared to right region(s) file(s) in search of overlaps. (BAM/BED/GFF/VCF formatted)
* ``right``: Path or list of paths to region(s) file(s) (BAM/BED/GFF/VCF formatted)

**Output:**

* Path to the intersection.



Params
------

* ``extra``: additional program arguments (except `-a` (left) and `-b` (right))




Authors
-------

* Jan Forster


Code
----

.. code-block:: python

    __author__ = "Jan Forster"
    __copyright__ = "Copyright 2019, Jan Forster"
    __email__ = "j.forster@dkfz.de"
    __license__ = "MIT"

    from snakemake.shell import shell

    ## Extract arguments
    extra = snakemake.params.get("extra", "")
    log = snakemake.log_fmt_shell(stdout=True, stderr=True)

    shell(
        "(bedtools intersect"
        " {extra}"
        " -a {snakemake.input.left}"
        " -b {snakemake.input.right}"
        " > {snakemake.output})"
        " {log}"
    )


.. |nl| raw:: html

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