.. _`bio/ragtag/patch`:

RAGTAG-PATH
===========


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

Homology-based assembly patching.

**URL**: https://github.com/malonge/RagTag/wiki/patch

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule patch:
        input:
            query="fasta/{query}.fasta",
            ref="fasta/{reference}.fasta",
        output:
            agp="{query}_{reference}.agp",
            fasta="{query}_{reference}.fasta",
            rename_agp="{query}_{reference}.rename.agp",
            rename_fasta="{query}_{reference}.rename.fasta",
            ctg_agp="{query}_{reference}.ctg.agp",
            ctg_fasta="{query}_{reference}.ctg.fasta",
            comps_fasta="{query}_{reference}.comps.fasta",
            asm_dir=directory("{query}_{reference}_asm"),  # Assembly alignment files
        params:
            extra="",
        threads: 16
        log:
            "logs/ragtag/{query}_patch_{reference}.log",
        wrapper:
            "v3.0.1/bio/ragtag/patch"

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
-----

Multiple threads can be used during Minimap/Unimap alignment.

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

* ``ragtag=2.1.0``

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

* ``ref``: reference fasta file (uncompressed or bgzipped)
* ``query``: query fasta file (uncompressed or bgzipped)

**Output:**

* ``fasta``: The final FASTA file containing the patched assembly
* ``agp``: The final AGP file defining how ragtag.patch.fasta is built.
* ``rename_agp``: Optional. An AGP file defining the new names for query sequences
* ``rename_fasta``: Optional. A FASTA file with the original query sequence, but with new names.
* ``comps_fasta``: Optional. The split target assembly and the renamed query assembly combined into one FASTA file.
* ``ctg_agp``: Optional. An AGP file defining how the target assembly was split at gaps
* ``ctg_fasta``: Optional. The target assembly split at gaps
* ``asm_dir``: Optional. A directory containing Assembly alignment files.



Params
------

* ``extra``: additional parameters




Authors
-------

* Curro Campuzano Jiménez


Code
----

.. code-block:: python

    """Snakemake wrapper for ragtag-patch."""

    __author__ = "Curro Campuzano Jiménez"
    __copyright__ = "Copyright 2023, Curro Campuzano Jiménez"
    __email__ = "campuzanocurro@gmail.com"
    __license__ = "MIT"

    import tempfile
    from snakemake.shell import shell


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

    assert snakemake.output.keys(), "Output must contain at least one named file."

    valid_keys = [
        "agp",
        "fasta",
        "rename_agp",
        "rename_fasta",
        "comps_fasta",
        "ctg_agp",
        "ctg_fasta",
        "asm_dir",
    ]
    for key in snakemake.output.keys():
        assert (
            key in valid_keys
        ), "Invalid key in output. Valid keys are: %r. Given: %r." % (valid_keys, key)

    with tempfile.TemporaryDirectory() as tmpdir:
        shell(
            "ragtag.py patch"
            " {snakemake.input.ref}"
            " {snakemake.input.query}"
            " {extra}"
            " -o {tmpdir} -t {snakemake.threads}"
            " {log}"
        )
        for key in valid_keys[:-1]:
            outfile = snakemake.output.get(key)
            if outfile:
                extension = key.replace("_", ".")
                shell("mv {tmpdir}/ragtag.patch.{extension} {outfile}")
        outdir = snakemake.output.get("asm_dir")
        if outdir:
            # Move files into directory outdir
            shell("mkdir -p {outdir} && mv {tmpdir}/ragtag.patch.asm.* {outdir}")


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