.. _`bio/deeptools/bamcoverage`:

DEEPTOOLS BAMCOVERAGE
=====================


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

``deepTools bamcoverage`` takes an alignment of reads or fragments as input (BAM file) and generates a coverage track (bigWig or bedGraph) as output.  For more information about ``deepTools``, also see the `source code <https://github.com/deeptools/deepTools>`_.


**URL**: https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html?highlight=bamcoverage

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule test_deeptools_bamcoverage:
        input:
            bam="a.sorted.bam",
            bai="a.sorted.bam.bai",
            # Optional path to a blacklist bed file
            # blacklist="",
        output:
            "a.coverage.bw",
        params:
            effective_genome_size=1000,
            extra="",
        log:
            "logs/coverage.log",
        wrapper:
            "v3.0.1/bio/deeptools/bamcoverage"

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

* ``deeptools=3.5.4``

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

* ``bam``: Path to alignment (BAM) file
* ``blacklist``: Path to optional blacklist region file (BED)

**Output:**

* Path to coverage file



Params
------

* ``effective_genome_size``: Optional effective genome size value

* ``genome``: Optional parameter used to fill effective genome size with pre-computed parameters. Can only be one of `GRCm37`, `GRCm38`, `GRCh37`, `GRCh38`, `dm3`, `dm6`, `WBcel235`, or `GRCz10`.

* ``read_length``: Optional parameter used to fill effective genome size with pre-computed parameters. Can only be one of `50`, `75`, `100`, `150`, or `200`.

* ``extra``: Optional parameters to be given to deepTools bamcoverage




Authors
-------

* Thibault Dayris


Code
----

.. code-block:: python

    __author__ = "Thibault Dayris"
    __copyright__ = "Copyright 2022, Thibault Dayris"
    __email__ = "thibault.dayris@gustaveroussy.fr"
    __license__ = "MIT"

    from snakemake.shell import shell

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

    # See: https://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html
    default_effective_genome_size = {
        "GRCz10": {
            "50": 1195445591,
            "75": 1251132686,
            "100": 1280189044,
            "150": 1312207169,
            "200": 1321355241,
        },
        "WBcel235": {
            "50": 95159452,
            "75": 96945445,
            "100": 98259998,
            "150": 98721253,
            "200": 98672758,
        },
        "dm3": {
            "50": 130428560,
            "75": 135004462,
            "100": 139647232,
            "150": 144307808,
            "200": 148524010,
        },
        "dm6": {
            "50": 125464728,
            "75": 127324632,
            "100": 129789873,
            "150": 129941135,
            "200": 132509163,
        },
        "GRCh37": {
            "50": 2685511504,
            "75": 2736124973,
            "100": 2776919808,
            "150": 2827437033,
            "200": 2855464000,
        },
        "GRCh38": {
            "50": 2701495761,
            "75": 2747877777,
            "100": 2805636331,
            "150": 2862010578,
            "200": 2887553303,
        },
        "GRCm37": {
            "50": 2304947926,
            "75": 2404646224,
            "100": 2462481010,
            "150": 2489384235,
            "200": 2513019276,
        },
        "GRCm38": {
            "50": 2308125349,
            "75": 2407883318,
            "100": 2467481108,
            "150": 2494787188,
            "200": 2520869189,
        },
    }

    effective_genome_size = snakemake.params.get("effective_genome_size")
    if not effective_genome_size:
        genome = snakemake.params.get("genome")
        read_length = snakemake.params.get("read_length")
        if genome and read_length:
            effective_genome_size = "--effectiveGenomeSize "
            effective_genome_size += default_effective_genome_size[genome][str(read_length)]
    else:
        effective_genome_size = "--effectiveGenomeSize " + str(effective_genome_size)


    output_format = ""
    bigwig_format = ["bw", "bigwig"]
    bedgraph_format = ["bg", "bedgraph"]
    output_ext = str(snakemake.output[0]).split(".")[-1].lower()
    if output_ext in bigwig_format:
        output_format = "bigwig"
    elif output_ext in bedgraph_format:
        output_format = "bedgraph"
    else:
        raise ValueError("Output file should be either a bigwig or a bedgraph file")


    blacklist = snakemake.input.get("blacklist", "")
    if blacklist:
        blacklist = "--blackListFileName " + blacklist

    shell(
        "bamCoverage "
        "{blacklist} {extra} "
        "--numberOfProcessors {snakemake.threads} "
        "{effective_genome_size} "
        "--bam {snakemake.input.bam} "
        "--outFileName {snakemake.output} "
        "--outFileFormat {output_format} "
        "{log} "
    )


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