.. _`bio/ucsc/faToTwoBit`:

FATOTWOBIT
==========


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

Convert \*.fa file to \*.2bit 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

    # Example: from *.fa file
    rule faToTwoBit_fa:
        input:
            "{sample}.fa"
        output:
            "{sample}.2bit"
        log:
            "logs/{sample}.fa_to_2bit.log"
        params:
            "" # optional params string
        wrapper:
            "v3.0.4/bio/ucsc/faToTwoBit"

    # Example: from *.fa.gz file
    rule faToTwoBit_fa_gz:
        input:
            "{sample}.fa.gz"
        output:
            "{sample}.2bit"
        log:
            "logs/{sample}.fa-gz_to_2bit.log"
        params:
            "" # optional params string
        wrapper:
            "v3.0.4/bio/ucsc/faToTwoBit"

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-fatotwobit=455``

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

* Path(s) to genome \*.fa or \*.fa.gz files

**Output:**

* Path to output '\*.2bit' file




Authors
-------

* Roman Cherniatchik


Code
----

.. code-block:: python

    """Snakemake wrapper for *.2bit to *.fa conversion using UCSC faToTwoBit 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("faToTwoBit {extra} {snakemake.input} {snakemake.output} {log}")


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