.. _`bio/bismark/bismark2bedGraph`:

BISMARK2BEDGRAPH
================


.. image:: https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/bismark/bismark2bedGraph?label=version%20update%20pull%20requests
   :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Abio/bismark/bismark2bedGraph

Generate bedGraph and coverage files from positional methylation files created by bismark_methylation_extractor (see https://github.com/FelixKrueger/Bismark/blob/master/bismark2bedGraph).



Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    # Example for CHG+CHH summary coverage:
    rule bismark2bedGraph_noncpg:
        input:
            "meth/CHG_context_{sample}.txt.gz",
            "meth/CHH_context_{sample}.txt.gz"
        output:
            bedGraph="meth_non_cpg/{sample}_non_cpg.bedGraph.gz",
            cov="meth_non_cpg/{sample}_non_cpg.bismark.cov.gz"
        log:
            "logs/meth_non_cpg/{sample}_non_cpg.log"
        params:
            extra="--CX"
        wrapper:
            "v3.0.4/bio/bismark/bismark2bedGraph"

    # Example for CpG only coverage
    rule bismark2bedGraph_cpg:
        input:
            "meth/CpG_context_{sample}.txt.gz"
        output:
            bedGraph="meth_cpg/{sample}_CpG.bedGraph.gz",
            cov="meth_cpg/{sample}_CpG.bismark.cov.gz"
        log:
            "logs/meth_cpg/{sample}_CpG.log"
        wrapper:
            "v3.0.4/bio/bismark/bismark2bedGraph"

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

* ``bowtie2=2.5.2``
* ``bismark=0.24.2``
* ``samtools=1.18``

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

* Files generated by bismark_methylation_extractor, e.g. CpG_context\*.txt.gz, CHG_context\*.txt.gz, CHH_context\*.txt.gz. By default only CpG file is required, if '--CX' option is output is build by merged input files.

**Output:**

* ``bedGraph``: Bismark methylation level track, \*.bedGraph.gz (0-based start, 1-based end coordintates, i.e. end offset exclusive)
* ``cov``: Optional bismark coverage file \*.bismark.cov.gz, file name is calculated by bedGraph name (1-based start and end, i.e. end offset inclusive)



Params
------

* ``extra``: Any additional args, e.g. '--CX', '--ample_memory', ' --buffer_size 10G', etc.




Authors
-------

* Roman Cherniatchik


Code
----

.. code-block:: python

    """Snakemake wrapper for Bismark bismark2bedGraph tool."""
    # https://github.com/FelixKrueger/Bismark/blob/master/bismark2bedGraph

    __author__ = "Roman Chernyatchik"
    __copyright__ = "Copyright (c) 2019 JetBrains"
    __email__ = "roman.chernyatchik@jetbrains.com"
    __license__ = "MIT"


    import os
    from snakemake.shell import shell

    bedGraph = snakemake.output.get("bedGraph", "")
    if not bedGraph:
        raise ValueError("bismark/bismark2bedGraph: Please specify bedGraph output path")

    params_extra = snakemake.params.get("extra", "")
    cmdline_args = ["bismark2bedGraph {params_extra}"]

    dir_name = os.path.dirname(bedGraph)
    if dir_name:
        cmdline_args.append("--dir {dir_name}")

    fname = os.path.basename(bedGraph)
    cmdline_args.append("--output {fname}")

    cmdline_args.append("{snakemake.input}")

    log = snakemake.log_fmt_shell(stdout=True, stderr=True)
    cmdline_args.append("{log}")

    # run
    shell(" ".join(cmdline_args))


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