.. _`bio/gatk/modelsegments`:

GATK MODELSEGMENTS
==================


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

Models segmented copy ratios from denoised copy ratios and segmented minor-allele fractions from allelic counts


**URL**: https://gatk.broadinstitute.org/hc/en-us/articles/13832747657883-ModelSegments

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule modelsegments_denoise_input:
        input:
            denoised_copy_ratios="a.denoisedCR.tsv",
        output:
            "a.den.modelFinal.seg",
            "a.n.cr.seg",
        log:
            "logs/gatk/modelsegments_denoise.log",
        params:
            #prefix="a.den.test",
            extra="",  # optional
            java_opts="",  # optional
        resources:
            mem_mb=1024,
        wrapper:
            "v3.0.1/bio/gatk/modelsegments"

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

* ``gatk4=4.4.0.0``
* ``snakemake-wrapper-utils=0.6.2``

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

* ``denoised_copy_ratios``: denoised_copy_ratios file (optional)
* ``allelic_counts``: allelic_counts file (optional)
* ``normal_allelic_counts``: matched_normal allelic-counts (optional)
* ``segments``: segments Picard interval-list file containing a multisample segmentation output by a previous run (optional)

**Output:**

* list of files ending with either '.modelFinal.seq', '.cr.seg', '.af.igv.seg', '.cr.igv.seg', '.hets.tsv', '.modelBegin.cr.param', '.modelBegin.af.param', '.modelBegin.seg', '.modelFinal.af.param' or '.modelFinal.cr.param'



Params
------

* ``java_opts``: additional arguments to be passed to the java compiler, e.g. "-XX:ParallelGCThreads=10" (not for `-XmX` or `-Djava.io.tmpdir`, since they are handled automatically).

* ``extra``: additional program arguments.




Authors
-------

* Patrik Smeds


Code
----

.. code-block:: python

    __author__ = "Patrik Smeds"
    __copyright__ = "Copyright 2023, Patrik Smed"
    __email__ = "patrik.smeds@gmail.com"
    __license__ = "MIT"

    import os
    import tempfile
    from snakemake.shell import shell
    from snakemake_wrapper_utils.java import get_java_opts


    denoised_copy_ratios = ""
    if snakemake.input.get("denoised_copy_ratios", None):
        denoised_copy_ratios = (
            f"--denoised-copy-ratios {snakemake.input.denoised_copy_ratios}"
        )

    allelic_counts = ""
    if snakemake.input.get("allelic_counts", None):
        allelic_counts = f"--allelic-counts {snakemake.input.allelic_counts}"

    normal_allelic_counts = ""
    if snakemake.input.get("normal_allelic_counts", None):
        matched_normal_allelic_counts = (
            f"--normal-allelic-counts {snakemake.inut.normal_allelic_counts}"
        )

    segments = ""
    if snakemake.input.get("segments", None):
        interval_list = f"--segments {snakemake.input.segments}"

    if not allelic_counts and not denoised_copy_ratios:
        raise Exception(
            "wrapper input requires either 'allelic_counts' or 'denoise_copy_ratios' to be set"
        )

    if normal_allelic_counts and not allelic_counts:
        raise Exception(
            "'allelica_counts' is required when 'normal-allelic-counts' is an input to the rule!"
        )

    extra = snakemake.params.get("extra", "")
    java_opts = get_java_opts(snakemake)

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


    with tempfile.TemporaryDirectory() as tmpdir:
        output_folder = os.path.join(tmpdir, "output_folder")
        shell(
            "gatk --java-options '{java_opts}' ModelSegments"
            " {segments}"
            " {denoised_copy_ratios}"
            " {allelic_counts}"
            " {normal_allelic_counts}"
            " --output-prefix temp_name__"
            " -O {output_folder}"
            " --tmp-dir {tmpdir}"
            " {extra}"
            " {log}"
        )

        created_files = {}
        # Find all created files
        for new_file in os.listdir(output_folder):
            file_path = os.path.join(output_folder, new_file)
            if os.path.isfile(file_path):
                file_end = os.path.basename(file_path).split("__")[1]
                created_files[file_end] = file_path

        # Match expected output with found files
        for output in snakemake.output:
            file_found = False
            for file_ending in created_files:
                if output.endswith(file_ending):
                    shell(f"cp {created_files[file_ending]} {output}")
                    file_found = True
                    break
            if not file_found:
                created_files_list = [f"{e}" for e in created_files]
                raise IOError(
                    f"Could not create file {output}, possible files ends with {created_files_list}"
                )


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