.. _`bio/bedtools/genomecov`:

GENOMECOVERAGEBED
=================


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

Computes the coverage of a feature file as histograms, per-base reports or BEDGRAPH summaries among a given genome.


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

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule genomecov_bam:
        input:
            "bam_input/{sample}.sorted.bam"
        output:
            "genomecov_bam/{sample}.genomecov"
        log:
            "logs/genomecov_bam/{sample}.log"
        params:
            "-bg"  # optional parameters
        wrapper:
            "v3.0.4/bio/bedtools/genomecov"

    rule genomecov_bed:
        input:
            # for genome file format please see:
            # https://bedtools.readthedocs.io/en/latest/content/general-usage.html#genome-file-format
            bed="bed_input/{sample}.sorted.bed",
            ref="bed_input/genome_file"
        output:
            "genomecov_bed/{sample}.genomecov"
        log:
            "logs/genomecov_bed/{sample}.log"
        params:
            "-bg"  # optional parameters
        wrapper:
            "v3.0.4/bio/bedtools/genomecov"

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:**

* BED/GFF/VCF files grouped by chromosome and genome file (`genome file format <https://bedtools.readthedocs.io/en/latest/content/general-usage.html#genome-file-format>`_) OR
* BAM files sorted by position.
* ``ref``: Path to genome file, this must come after the other files

**Output:**

* genomecov (.genomecov)



Params
------

* ``extra``: additional program arguments




Authors
-------

* Antonie Vietor


Code
----

.. code-block:: python

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

    import os
    from snakemake.shell import shell

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

    genome = ""
    input_file = ""

    if (os.path.splitext(snakemake.input[0])[-1]) == ".bam":
        input_file = "-ibam " + snakemake.input[0]

    if len(snakemake.input) > 1:
        if (os.path.splitext(snakemake.input[0])[-1]) == ".bed":
            input_file = "-i " + snakemake.input.get("bed")
            genome = "-g " + snakemake.input.get("ref")

    shell(
        "(genomeCoverageBed"
        " {snakemake.params}"
        " {input_file}"
        " {genome}"
        " > {snakemake.output[0]}) {log}"
    )


.. |nl| raw:: html

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