.. _`bio/pyfastaq/replace_bases`:

PYFASTAQ REPLACE_BASES
======================


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

Replaces all occurrences of one letter with another.


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule replace_bases:
        input:
            "{sample}.rna.fa"
        output:
            "{sample}.dna.fa",
        params:
            old_base = "U",
            new_base = "T",
        log:
            "logs/fastaq/replace_bases/test/{sample}.log"
        wrapper:
            "v3.0.1/bio/pyfastaq/replace_bases"

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

* ``pyfastaq=3.17.0``




Authors
-------

* Michael Hall


Code
----

.. code-block:: python

    __author__ = "Michael Hall"
    __copyright__ = "Copyright 2019, Michael Hall"
    __email__ = "michael@mbh.sh"
    __license__ = "MIT"


    from snakemake.shell import shell


    log = snakemake.log_fmt_shell(stdout=False, stderr=True)

    shell(
        "fastaq replace_bases"
        " {snakemake.input[0]}"
        " {snakemake.output[0]}"
        " {snakemake.params.old_base}"
        " {snakemake.params.new_base}"
        " {log}"
    )


.. |nl| raw:: html

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