.. _`bio/paladin/align`:

PALADIN ALIGN
=============


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

Align nucleotide reads to a protein fasta file (that has been indexed with paladin index). 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_align:
        input:
            reads=["reads/reads.left.fq.gz"],
            index="index/prot.fasta.bwt",
        output:
            "paladin_mapped/{sample}.bam" # will output BAM format if output file ends with ".bam", otherwise SAM format
        log:
            "logs/paladin/{sample}.log"
        threads: 4
        wrapper:
            "v3.0.1/bio/paladin/align"

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:**

* nucleotide reads (fastq)
* indexed protein fasta file (output of paladin index or prepare)

**Output:**

* mapped reads (SAM or BAM format)




Authors
-------

* N. Tessa Pierce


Code
----

.. code-block:: python

    """Snakemake wrapper for PALADIN alignment"""

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

    from os import path
    from snakemake.shell import shell

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

    r = snakemake.input.get("reads")
    assert (
        r is not None
    ), "reads are required as input. If you have paired end reads, please merge them first (e.g. with PEAR)"
    index = snakemake.input.get("index")
    assert (
        index is not None
    ), "please index your assembly and provide the basename (with'.bwt' extension) via the 'index' input param"

    index_base = str(index).rsplit(".bwt")[0]

    outfile = snakemake.output

    # if bam output, pipe to bam!
    output_cmd = "  | samtools view -Sb - > " if str(outfile).endswith(".bam") else " -o "

    min_orf_len = snakemake.params.get("f", "250")

    shell(
        "paladin align -f {min_orf_len} -t {snakemake.threads} {extra} {index_base} {r} {output_cmd} {outfile}"
    )


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