.. _`bio/cooltools/genome/binnify`:

COOLTOOLS GENOME_BINNIFY
========================


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

Split chromosomes into equal sized bins

**URL**: https://github.com/open2c/cooltools

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule cooltools_genome_binnify:
        input:
            chromsizes="hg38_chromsizes.txt",  ## Chromsizes file
        output:
            "hg38_1000000_bins.bed",
        params:
            binsize=1000000,
        threads: 1
        log:
            "logs/binnify.log",
        wrapper:
            "v3.0.1/bio/cooltools/genome/binnify"

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

* ``cooltools=0.5.4``

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

* a chromsizes file

**Output:**

* A .bed file with bin coordinates.  Can have a {binsize} wildcard that specifies the resolution for the analysis, then it doesn't need to be specified as a parameter.




Params
------

* ``binsize``: size of bins in bp. Optional, can be instead specified as a wildcard in the output

* ``extra``: Any additional arguments to pass




Authors
-------

* Ilya Flyamer


Code
----

.. code-block:: python

    __author__ = "Ilya Flyamer"
    __copyright__ = "Copyright 2022, Ilya Flyamer"
    __email__ = "flyamer@gmail.com"
    __license__ = "MIT"

    from snakemake.shell import shell

    ## Extract arguments
    binsize = snakemake.params.get("binsize", snakemake.wildcards.get("binsize", 0))
    if not binsize:
        raise ValueError("Please specify binsize either as a wildcard or as a parameter")

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


    shell(
        "(cooltools genome binnify"
        " {snakemake.input.chromsizes} {binsize} "
        " {extra} "
        " > {snakemake.output}) {log}"
    )


.. |nl| raw:: html

   <br>