.. _`bio/diamond/blastp`:

DIAMOND BLASTP
==============


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

DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data.

**URL**: https://github.com/bbuchfink/diamond/wiki

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule diamond_blastp:
        input:
            fname_fasta="{sample}.fasta",  # Query fasta file
            fname_db="db.dmnd",  # Diamond db
        output:
            fname="{sample}.tsv.gz",  # Output file
        log:
            "logs/diamond_blastp/{sample}.log",
        params:
            extra="--header --compress 1",  # Additional arguments
        threads: 8
        wrapper:
            "v3.0.1/bio/diamond/blastp"

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

* ``diamond=2.1.8``

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

* ``fname_fasta``: Path to query file (Fasta formatted)
* ``fname_db``: Path to diamon database

**Output:**

* ``fname``: Path to query results



Params
------

* ``extra``: Optional parameters, besides `--threads`, `--db`, `--query`, and `--out`.




Authors
-------

* Nikos Tsardakas Renhuldt
* Kim Philipp Jablonski


Code
----

.. code-block:: python

    __author__ = "Kim Philipp Jablonski, Nikos Tsardakas Renhuldt"
    __copyright__ = "Copyright 2020, Kim Philipp Jablonski, Nikos Tsardakas Renhuldt"
    __email__ = "kim.philipp.jablonski@gmail.com, nikos.tsardakas_renhuldt@tbiokem.lth.se"
    __license__ = "MIT"


    from snakemake.shell import shell


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


    shell(
        "diamond blastp"
        " --threads {snakemake.threads}"
        " --db {snakemake.input.fname_db}"
        " --query {snakemake.input.fname_fasta}"
        " --out {snakemake.output.fname}"
        " {extra}"
        " {log}"
    )


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