.. _`bio/plass`:

PLASS
=====


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

Plass (Protein-Level ASSembler) is software to assemble short read sequencing data on a protein level. The main purpose of Plass is the assembly of complex metagenomic datasets.


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule plass_paired:
        input:
            left=["reads/reads.left.fq.gz", "reads/reads2.left.fq.gz"],
            right=["reads/reads.right.fq.gz", "reads/reads2.right.fq.gz"]
        output:
            "plass/prot.fasta"
        log:
            "logs/plass.log"
        params:
            extra=""
        threads: 4
        wrapper:
            "v3.0.1/bio/plass"

    rule plass_single:
        input:
            single=["reads/reads.left.fq.gz", "reads/reads2.left.fq.gz"],
        output:
            "plass/prot_single.fasta"
        log:
            "logs/plass_single.log"
        params:
            extra=""
        threads: 4
        wrapper:
            "v3.0.1/bio/plass"

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

* ``plass=4.687d7``

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

* fastq files

**Output:**

* fasta containing protein assembly




Authors
-------

* N. Tessa Pierce


Code
----

.. code-block:: python

    """Snakemake wrapper for PLASS Protein-Level Assembler."""

    __author__ = "N. Tessa Pierce"
    __copyright__ = "Copyright 2018, N. Tessa Pierce"
    __email__ = "ntpierce@gmail.com"
    __license__ = "MIT"

    from os import path
    from snakemake.shell import shell

    extra = snakemake.params.get("extra", "")

    # allow multiple input files for single assembly
    left = snakemake.input.get("left")
    single = snakemake.input.get("single")
    assert (
        left is not None or single is not None
    ), "please check read inputs: either left/right or single read file inputs are required"
    if left:
        left = (
            [snakemake.input.left]
            if isinstance(snakemake.input.left, str)
            else snakemake.input.left
        )
        right = snakemake.input.get("right")
        assert (
            right is not None
        ), "please input 'right' reads or specify that the reads are 'single'"
        right = (
            [snakemake.input.right]
            if isinstance(snakemake.input.right, str)
            else snakemake.input.right
        )
        assert len(left) == len(
            right
        ), "left input needs to contain the same number of files as the right input"
        input_str_left = " " + " ".join(left)
        input_str_right = " " + " ".join(right)
        input_cmd = input_str_left + " " + input_str_right
    else:
        single = (
            [snakemake.input.single]
            if isinstance(snakemake.input.single, str)
            else snakemake.input.single
        )
        input_cmd = " " + " ".join(single)


    outdir = path.dirname(snakemake.output[0])
    tmpdir = path.join(outdir, "tmp")

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

    shell(
        "plass assemble {input_cmd} {snakemake.output} {tmpdir} --threads {snakemake.threads} {snakemake.params.extra} {log}"
    )


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