.. _`bio/hmmer/hmmbuild`:

HMMBUILD
========


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

hmmbuild: construct profile HMM(s) from multiple sequence alignment(s)


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule hmmbuild_profile:
        input:
            "test-profile.sto"
        output:
            "test-profile.hmm"
        log:
            "logs/test-profile-hmmbuild.log"
        params:
            extra="",
        threads: 4
        wrapper:
            "v3.0.1/bio/hmmer/hmmbuild"

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

* ``hmmer=3.4``

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

* sequence alignment file

**Output:**

* profile hmm




Authors
-------

* N Tessa Pierce


Code
----

.. code-block:: python

    """Snakemake wrapper for hmmbuild"""

    __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)

    shell(
        " hmmbuild {extra} --cpu {snakemake.threads} "
        " {snakemake.output} {snakemake.input} {log} "
    )


.. |nl| raw:: html

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