.. _`bio/gfatools`:

GFATOOLS
========


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

Tools for manipulating sequence graphs in the GFA and rGFA formats


**URL**: https://github.com/lh3/gfatools

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule gfatools_stat:
        input:
            "{sample}.gfa",
        output:
            "{sample}.stat",
        log:
            "logs/{sample}.stat.log",
        params:
            command="stat",
        wrapper:
            "v3.0.1/bio/gfatools"


    rule gfatools_gfa2fa:
        input:
            "{sample}.gfa",
        output:
            "{sample}.fas",
        log:
            "logs/{sample}.gfa2fa.log",
        params:
            command="gfa2fa",
    	extra="-l 90",
        wrapper:
            "v3.0.1/bio/gfatools"


    rule gfatools_gfa2bed:
        input:
            "{sample}.gfa",
        output:
            "{sample}.bed",
        log:
            "logs/{sample}.gfa2bed.log",
        params:
            command="gfa2bed",
        wrapper:
            "v3.0.1/bio/gfatools"


    rule gfatools_blacklist:
        input:
            "{sample}.gfa",
        output:
            "{sample}.blacklist",
        log:
            "logs/{sample}.blacklist.log",
        params:
            command="blacklist",
    	extra="-l 100",
        wrapper:
            "v3.0.1/bio/gfatools"


    rule gfatools_bubble:
        input:
            "{sample}.gfa",
        output:
            "{sample}.bubble",
        log:
            "logs/{sample}.bubble.log",
        params:
            command="bubble",
        wrapper:
            "v3.0.1/bio/gfatools"


    rule gfatools_asm:
        input:
            "{sample}.gfa",
        output:
            "{sample}.asm",
        log:
            "logs/{sample}.asm.log",
        params:
            command="asm",
    	extra="-u",
        wrapper:
            "v3.0.1/bio/gfatools"


    rule gfatools_sql:
        input:
            "{sample}.gfa",
        output:
            "{sample}.sql",
        log:
            "logs/{sample}.sql.log",
        params:
            command="sql",
        wrapper:
            "v3.0.1/bio/gfatools"

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.


Notes
-----

* The `command` param allows to specify how to do with the GFA: `view` [default], `stat`, `gfa2fa`, `gfa2bed`, `blacklist`, `bubble`, `asm`, `sql`, or `version`.


Software dependencies
---------------------

* ``gfatools=0.5``

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

* GFA file

**Output:**

* GFA/stats/FAS/BED/ASM/SQL/TXT (depends on command)




Authors
-------

* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Filipe G. Vieira"
    __copyright__ = "Copyright 2022, Filipe G. Vieira"
    __license__ = "MIT"


    from snakemake.shell import shell


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


    command = snakemake.params.get("command", "view")
    assert command in [
        "view",
        "stat",
        "gfa2fa",
        "gfa2bed",
        "blacklist",
        "bubble",
        "asm",
        "sql",
        "version",
    ], "invalid command specified."


    shell("gfatools {command} {extra} {snakemake.input[0]} > {snakemake.output[0]} {log}")


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