.. _`bio/microphaser/somatic`:

MICROPHASER SOMATIC
===================


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

Predict mutated neopeptides and their wildtype counterparts from NGS (whole exome/genome) data



Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule microphaser_somatic:
        input:
            bam="mapped/{sample}.sorted.bam",
            index="mapped/{sample}.sorted.bam.bai",
            ref="genome.fasta",
            annotation="genome.gtf",
            variants="calls/{sample}.bcf",
        output:
            # sequences neopeptides arisen from somatic variants
            tumor="out/{sample}.mt.fasta",
            # sequences of the normal, unmutated counterpart to every neopeptide
            normal="out/{sample}.wt.fasta",
            # info data of the somatic neopeptides
            tsv="out/{sample}.info.tsv",
        log:
            "logs/microphaser/somatic/{sample}.log",
        params:
            extra="--window-len 9",  # optional, desired peptide length in nucleotide bases, e.g. 27 (9 AA) for MHC-I ligands.
        wrapper:
            "v3.0.1/bio/microphaser/somatic"

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
-----

* For more information see, https://github.com/koesterlab/microphaser.


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

* ``microphaser=0.8.0``

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

* bam file
* bcf file
* fasta reference
* gtf annotation file

**Output:**

* mutated peptide fasta (nucleotide sequences)
* wildtype peptide fasta (nucleotide sequences)
* information tsv




Authors
-------

* Jan Forster


Code
----

.. code-block:: python

    __author__ = "Jan Forster"
    __copyright__ = "Copyright 2021, Jan Forster"
    __license__ = "MIT"


    from snakemake.shell import shell

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

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

    shell(
        "microphaser somatic {snakemake.input.bam} "
        "{extra} "
        "--ref {snakemake.input.ref} "
        "--variants {snakemake.input.variants} "
        "--normal-output {snakemake.output.normal} "
        "--tsv {snakemake.output.tsv} "
        "> {snakemake.output.tumor} "
        "< {snakemake.input.annotation} "
        "{log}"
    )


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