.. _`bio/mashmap`:

MASHMAP
=======


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

Compute local alignment boundaries between long DNA sequences with MashMap

**URL**: https://github.com/marbl/MashMap

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule test_mashmap:
        input:
            ref="reference.fasta.gz",  # This can be a txt file with a path to a fasta-file per line
            query="read.fasta.gz",
        output:
            "mashmap.out",
        threads: 2
        params:
            extra="-s 1000 --pi 99",
        log:
            "logs/mashmap.log",
        wrapper:
            "v3.0.1/bio/mashmap"

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
-----

* `input.ref` may be either a path to a fasta file or a text file containing a list of paths to several fasta files.
* `input.query` may be either a path to a fastq file or a text file containing a list of paths to several fastq files.

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

* ``mashmap=3.1.1``
* ``gsl=2.7``
* ``gzip=1.13``

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

* ``ref``: Path to reference file
* ``query``: Path to query file (fasta, fastq)

**Output:**

* Path to the alignment file



Params
------

* ``extra``: Optional parameters for MashMap




Authors
-------

* Thibault Dayris


Code
----

.. code-block:: python

    #!/usr/bin/python3.8
    # coding: utf-8

    """ Snakemake wrapper for MashMap """

    __author__ = "Thibault Dayris"
    __copyright__ = "Copyright 2022, Thibault Dayris"
    __email__ = "thibault.dayris@gustaveroussy.fr"
    __license__ = "MIT"

    from snakemake.shell import shell

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

    # Handling input file types (either a fasta file, or a text file with a list of paths to fasta files)
    ref = snakemake.input["ref"]
    if ref.endswith(".txt"):
        ref = f"--refList {ref}"
    elif ref.endswith(".gz"):
        ref = f"--ref <( gzip --decompress --stdout {ref} )"
        max_threads -= 1
    else:
        ref = f"--ref {ref}"

    if max_threads < 1:
        raise ValueError(
            "Reference fasta on-the-fly g-unzipping consumed one thread."
            f" Please increase the number of available threads by {1 - max_threads}."
        )


    # Handling query file format (either a fastq file or a text file with a list of fastq files)
    query = snakemake.input["query"]
    if query.endswith(".txt"):
        query = f"--queryList {query}"
    else:
        query = f"--query {query}"

    shell(
        "mashmap "
        "{ref} "
        "{query} "
        "--output {snakemake.output} "
        "--threads {snakemake.threads} "
        "{extra} "
        "{log}"
    )


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