.. _`bio/verifybamid/verifybamid2`:

VERIFYBAMID2
============


.. image:: https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/verifybamid/verifybamid2?label=version%20update%20pull%20requests
   :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Abio/verifybamid/verifybamid2

Run verifybamid2.



Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule verify_bam_id:
        input:
            bam="a.bam",
            ref="genome.fasta",
            # optional - this can be used to specify custom resource files if
            # necessary (if using GRCh37 or GRCh38 instead simply specify
            # params.genome_build="38", for example)
            # N.B. if svd_mu={prefix}.mu, then {prefix}.bed, {prefix}.UD, and
            # {prefix}.V must also exist
            svd_mu="ref.vcf.mu",
        output:
            selfsm="a.selfSM",
            ancestry="a.ancestry",
        params:
            # optional - see note for input.svd_mu
            # current choices are {37,38}
            # genome_build="38",
        log:
            "logs/verifybamid2/a.log",
        wrapper:
            "v3.0.1/bio/verifybamid/verifybamid2"

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 `extra` param allows for additional program arguments.
* For more information see, https://github.com/Griffan/VerifyBamID


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

* ``verifybamid2=2.0.1``

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

* bam file

**Output:**

* estimated intraspacies contamination




Authors
-------

* Brett Copeland


Code
----

.. code-block:: python

    __author__ = "Brett Copeland"
    __copyright__ = "Copyright 2021, Brett Copeland"
    __email__ = "brcopeland@ucsd.edu"
    __license__ = "MIT"


    import os
    from tempfile import TemporaryDirectory
    from shutil import copyfile

    from snakemake.shell import shell

    extra = snakemake.params.get("extra", "")
    svd_mu = snakemake.input.get("svd_mu", "")
    if svd_mu:
        svd_prefix = os.path.splitext(svd_mu)[0]
        for suffix in ("bed", "UD", "V"):
            fn = f"{svd_prefix}.{suffix}"
            if not os.path.isfile(fn):
                raise Exception(f"Failed to find required input {fn}.")
    else:
        genome_build = snakemake.params.get("genome_build", "38")
        if genome_build not in ("37", "38"):
            raise Exception(
                f"No svd_prefix given and improper {genome_build=} "
                f"given.  Valid choices are 37,38."
            )
        verifybamid2_found = False
        for path in os.getenv("PATH").split(os.path.pathsep):
            path_to_verifybamid2 = os.path.join(path, "verifybamid2")
            if os.path.isfile(path_to_verifybamid2):
                verifybamid2_found = True
                resources_directory = os.path.join(
                    os.path.dirname(os.path.realpath(path_to_verifybamid2)), "resource"
                )
                svd_prefix = os.path.join(
                    resources_directory, f"1000g.phase3.100k.b{genome_build}.vcf.gz.dat"
                )
                break
        if not verifybamid2_found:
            raise Exception("Failed to find verifybamid2 location.")


    def move_file(src, dst):
        "this function will move `fn` while respecting ACLs in the target directory"
        copyfile(src, dst)
        os.remove(src)


    # verifybamid2 outputs results to result.selfSM and result.Ancestry in the working directory,
    # so to avoid collisions we have to run it from a temporary directory and fix the paths
    # to inputs, outputs, and the log file
    ref_path = os.path.abspath(snakemake.input.ref)
    svd_prefix = os.path.abspath(svd_prefix)
    bam_path = os.path.abspath(snakemake.input.bam)
    selfsm_path = os.path.abspath(snakemake.output.selfsm)
    ancestry_path = os.path.abspath(snakemake.output.ancestry)
    if snakemake.log:
        snakemake.log[0] = os.path.abspath(snakemake.log[0])
    log = snakemake.log_fmt_shell(stdout=True, stderr=True)
    with TemporaryDirectory() as tmp_dir:
        os.chdir(tmp_dir)
        shell(
            "verifybamid2 --SVDPrefix {svd_prefix} "
            "--Reference {ref_path} --BamFile {bam_path} {extra} "
            "--NumThread {snakemake.threads} {log}"
        )
        move_file("result.selfSM", selfsm_path)
        move_file("result.Ancestry", ancestry_path)


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