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

COOLTOOLS GENOME_GC
===================


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

Calculate GC content for a genome in bins

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

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule cooltools_genome_gc:
        input:
            bins="ASM584v2/bins_100000.bed",  # 100000 bins
            fasta="ASM584v2/ASM584v2.fa",  # genome fasta for E. coli
        output:
            "gc_100000.tsv",
        params:
            extra="",
        threads: 1
        log:
            "logs/gc.log",
        wrapper:
            "v3.0.1/bio/cooltools/genome/gc"

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:**

* .bed file with bin coordinates
* fasta file with the genome sequence

**Output:**

* A tsv file with GC content in bins




Params
------

* ``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
    extra = snakemake.params.get("extra", "")
    log = snakemake.log_fmt_shell(stdout=False, stderr=True)
    shell(
        "(cooltools genome gc"
        " {snakemake.input.bins} {snakemake.input.fasta} {extra} > {snakemake.output})"
        " {log} "
    )


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