.. _`bio/bwa-memx/index`:

BWA-MEM2 INDEX
==============


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

Creates a bwa-mem, bwa-mem2 or bwa-meme index.


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule bwa_mem_index:
        input:
            "{genome}",
        output:
            multiext(
                "{genome}",
                ".amb",
                ".ann",
                ".bwt",
                ".pac",
                ".sa",
            ),
        log:
            "logs/bwa-mem_index/{genome}.log",
        params:
            bwa="bwa-mem",
        threads: 8
        wrapper:
            "v3.0.1/bio/bwa-memx/index"


    rule bwa_mem2_index:
        input:
            "{genome}",
        output:
            multiext(
                "{genome}",
                ".0123",
                ".amb",
                ".ann",
                ".bwt.2bit.64",
                ".pac",
            ),
        log:
            "logs/bwa-mem2_index/{genome}.log",
        params:
            bwa="bwa-mem2",
        threads: 8
        wrapper:
            "v3.0.1/bio/bwa-memx/index"


    rule bwa_meme_index:
        input:
            "{genome}",
        output:
            multiext(
                "{genome}",
                ".0123",
                ".amb",
                ".ann",
                ".pac",
                ".pos_packed",
                ".suffixarray_uint64",
                ".suffixarray_uint64_L0_PARAMETERS",
                ".suffixarray_uint64_L1_PARAMETERS",
                ".suffixarray_uint64_L2_PARAMETERS",
            ),
        log:
            "logs/bwa-meme_index/{genome}.log",
        params:
            bwa="bwa-meme",
        threads: 8
        wrapper:
            "v3.0.1/bio/bwa-memx/index"

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

* ``bwa=0.7.17``
* ``bwa-mem2=2.2.1``
* ``bwa-meme=1.0.6``




Authors
-------

* Christopher Schröder
* Patrik Smeds


Code
----

.. code-block:: python

    __author__ = "Christopher Schröder, Patrik Smeds"
    __copyright__ = "Copyright 2022, Christopher Schröder, Patrik Smeds"
    __email__ = "christopher.schroeder@tu-dortmund.de, patrik.smeds@gmail.com"
    __license__ = "MIT"

    from os import path

    from snakemake.shell import shell

    log = snakemake.log_fmt_shell(stdout=True, stderr=True)

    bwa = snakemake.params.get("bwa", "bwa-mem")

    # Check inputs/arguments.
    if len(snakemake.input) == 0:
        raise ValueError("A reference genome has to be provided.")
    elif len(snakemake.input) > 1:
        raise ValueError("Please provide exactly one reference genome as input.")

    if bwa == "bwa-mem":
        valid_suffixes = {
            ".amb",
            ".ann",
            ".bwt",
            ".pac",
            ".sa",
        }
        cmd = "bwa index {prefix} {snakemake.input[0]}"
    elif bwa == "bwa-mem2":
        valid_suffixes = {
            ".0123",
            ".amb",
            ".ann",
            ".bwt.2bit.64",
            ".pac",
        }
        cmd = "bwa-mem2 index -p {prefix} {snakemake.input[0]}"
    elif bwa == "bwa-meme":
        valid_suffixes = {
            ".0123",
            ".amb",
            ".ann",
            ".pac",
            ".pos_packed",
            ".suffixarray_uint64",
            ".suffixarray_uint64_L0_PARAMETERS",
            ".suffixarray_uint64_L1_PARAMETERS",
            ".suffixarray_uint64_L2_PARAMETERS",
        }

        cmd = "bwa-meme index -a meme -p {prefix} {snakemake.input[0]} -t {snakemake.threads} && bwa-meme-train-prmi -t {snakemake.threads} --data-path {dirname} {suffixarray} {basename} pwl,linear,linear_spline {num_models}"
    else:
        raise ValueError(
            "Unexpected value for params.bwa ({}). Must be bwa-mem, bwa-mem2 or bwa-meme.".format(
                bwa
            )
        )


    def get_valid_suffix(path):
        for suffix in valid_suffixes:
            if path.endswith(suffix):
                return suffix


    prefixes = set()
    for s in snakemake.output:
        suffix = get_valid_suffix(s)
        if suffix is None:
            raise ValueError(f"{s} cannot be generated by bwa-meme index (invalid suffix).")
        prefixes.add(s[: -len(suffix)])

    if len(prefixes) != 1:
        raise ValueError("Output files must share common prefix up to their file endings.")
    (prefix,) = prefixes

    suffixarray = snakemake.input[0] + ".suffixarray_uint64"
    dirname = path.dirname(suffixarray)
    basename = path.basename(suffixarray)
    num_models = snakemake.params.get("num_models", 268435456)  # change only for testing!

    if not dirname:
        dirname = "."

    shell(f"({cmd}) {log}")


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