.. _`bio/paladin/prepare`:

PALADIN PREPARE
===============


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

Download and prepare uniprot refs for paladin mapping. PALADIN is a protein sequence alignment tool designed for the accurate functional characterization of metagenomes.


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule paladin_prepare:
        output:
            "uniprot_sprot.fasta.gz",
            "uniprot_sprot.fasta.gz.pro"
        log:
            "logs/paladin/prepare_sprot.log"
        params:
            reference_type=1, # 1=swiss-prot, 2=uniref90
        wrapper:
            "v3.0.1/bio/paladin/prepare"

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

* ``paladin=1.4.6``
* ``samtools=1.18``




Authors
-------

* N. Tessa Pierce


Code
----

.. code-block:: python

    """Snakemake wrapper for Paladin Prepare"""

    __author__ = "N. Tessa Pierce"
    __copyright__ = "Copyright 2019, N. Tessa Pierce"
    __email__ = "ntpierce@gmail.com"
    __license__ = "MIT"

    from snakemake.shell import shell

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

    reference_type = snakemake.params.get(
        "reference_type", "1"
    )  # download swissprot as default
    assert int(reference_type) in [1, 2]
    ref_type_cmd = "-r" + str(reference_type)

    shell("paladin prepare {ref_type_cmd} {extra} {log}")


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