.. _`bio/ucsc/bedGraphToBigWig`:

BEDGRAPHTOBIGWIG
================


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

Convert \*.bedGraph file to \*.bw file (see http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt)



Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule bedGraphToBigWig:
        input:
            bedGraph="{sample}.bedGraph",
            chromsizes="genome.chrom.sizes"
        output:
            "{sample}.bw"
        log:
            "logs/{sample}.bed-graph_to_big-wig.log"
        params:
            "" # optional params string
        wrapper:
            "v3.0.1/bio/ucsc/bedGraphToBigWig"

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

* ``ucsc-bedgraphtobigwig=445``

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

* ``bedGraph``: Path to \*.bedGraph file
* ``chromsizes``: Chrom sizes file, could be generated by twoBitInfo or downloaded from UCSC

**Output:**

* Path to output '\*.bw' file




Authors
-------

* Roman Cherniatchik


Code
----

.. code-block:: python

    """Snakemake wrapper for *.bedGraph to *.bw conversion using UCSC bedGraphToBigWig tool."""
    # http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt

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

    from snakemake.shell import shell

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

    shell(
        "bedGraphToBigWig {extra}"
        " {snakemake.input.bedGraph} {snakemake.input.chromsizes}"
        " {snakemake.output} {log}"
    )


.. |nl| raw:: html

   <br>