.. _`bio/ragtag/merge`:

RAGTAG-MERGE
============


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

Scaffold merging.


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

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule merge:
        input:
            fasta="input/{assembly}.fasta",
            agps=expand("input/{scaffold}.agp", scaffold=["scf1", "scf2"]),
            #bam = "input/Hi-C.bam",
        output:
            fasta="{assembly}_merged.fasta",
            agp="{assembly}_merged.agp",
            #links = "{assembly}_merged.links",
        params:
            extra="",
        log:
            "logs/ragtag/{assembly}_merged.log",
        wrapper:
            "v3.0.1/bio/ragtag/merge"

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

* ``ragtag=2.1.0``

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

* ``ref``: assembly fasta file (uncompressed or bgzipped).
* ``agps``: scaffolding AGP files.
* ``bam``: Optional. Hi-C alignments in BAM format.

**Output:**

* ``fasta``: The merged scaffolds in FASTA format.
* ``agp``: The merged scaffold results in AGP format.
* ``links``: Optional. If Hi-C alignments in BAM format were given.



Params
------

* ``extra``: additional parameters. Do not use with '-b', add the bam file to the input instead.




Authors
-------

* Curro Campuzano Jiménez


Code
----

.. code-block:: python

    """Snakemake wrapper for ragtag-merge."""

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


    from snakemake.shell import shell
    import tempfile


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

    fasta_file = snakemake.input.get("fasta")
    # Check fasta_file is no
    assert fasta_file, "Input must contain only one fasta file."

    agp_files = snakemake.input.get("agps")

    assert len(agp_files) >= 2, "Input must contain at least 2 agp files. Given: %r." % len(
        agp_files
    )

    bam_file = snakemake.input.get("bam")

    # Add Hi-C BAM file to params if present
    if bam_file:
        extra += f" -b {bam_file}"

    # Raise warning if links file is expected but no Hi-C BAM file is given
    if snakemake.output.get("links") and not bam_file:
        raise "Links file is present but no Hi-C BAM file is given."

    # Check that all keys in snakemake output are valid are either agp, fasta or links
    assert snakemake.output.keys(), "Output must contain at least one named file."
    valid_keys = ["agp", "fasta", "links"]
    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 merge"
            " {fasta_file}"
            " {agp_files}"
            " {extra}"
            " -o {tmpdir}"
            " {log}"
        )
        for key in valid_keys:
            outfile = snakemake.output.get(key)
            if outfile:
                shell("mv {tmpdir}/ragtag.merge.{key} {outfile}")


.. |nl| raw:: html

   <br>