.. _`bio/paladin/index`:

PALADIN INDEX
=============


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

Index a protein fasta file for mapping with paladin. 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_index:
        input:
            "prot.fasta",
        output:
            "index/prot.fasta.bwt"
        log:
            "logs/paladin/prot_index.log"
        params:
          reference_type=3
        wrapper:
            "v3.0.1/bio/paladin/index"

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``

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

* protein fasta file

**Output:**

* file indexed for paladin mapping




Authors
-------

* N. Tessa Pierce


Code
----

.. code-block:: python

    """Snakemake wrapper for Paladin Index."""

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


    # this wrapper temporarily copies your assembly into the output dir
    # so that all the paladin output files end up in the desired spot

    from snakemake.shell import shell

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

    input_assembly = snakemake.input
    annotation = snakemake.input.get("gff", "")
    paladin_index = str(snakemake.output)
    reference_type = snakemake.params.get("reference_type", "3")
    assert int(reference_type) in [1, 2, 3, 4]
    ref_type_cmd = "-r" + str(reference_type)

    output_base = paladin_index.rsplit(".bwt")[0]

    shell("cp {input_assembly} {output_base}")
    shell("paladin index {ref_type_cmd} {output_base} {annotation} {extra} {log}")
    shell("rm -f {output_base}")


.. |nl| raw:: html

   <br>