.. _`bio/microphaser/filter`:

MICROPHASER FILTER
==================


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

Translate and filter neopeptides from microphaser output



Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule microphaser_filter:
        input:
            # the info file of the tumor sample to filter
            tsv="somatic/info.tsv",
            # All normal peptides to filter against
            ref_peptides="germline/peptides.bin",
        output:
            # the filtered neopeptides
            tumor="out/peptides.mt.fasta",
            # the normal peptides matching the filtered neopeptides
            normal="out/peptides.wt.fasta",
            # the info data of the filtered neopeptides
            tsv="out/peptides.info.tsv",
            # the info data of the removed neopeptides
            removed_tsv="out/peptides.removed.tsv",
            # the removed neopeptides
            removed_fasta="out/peptides.removed.fasta",
        log:
            "logs/microphaser/filter.log",
        params:
            extra="--peptide-length 9",  # optional, desired peptide length in amino acids.
        wrapper:
            "v3.0.4/bio/microphaser/filter"

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:**

* neopeptides fasta (nucleotide sequences from microphaser somatic)
* information tsv (from microphaser somatic)
* sample-specific normal/wildtype pepetides (binary created using microphaser build)

**Output:**

* filtered neopeptides (removed self-identical peptides) in amino acid FASTA format
* corresponding normal peptides in amino acid FASTA format
* filtered information tsv
* self-identical peptides removed from the neopeptide set (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 filter "
        "{extra} "
        "--tsv {snakemake.input.tsv} "
        "--reference {snakemake.input.ref_peptides} "
        "--normal-output {snakemake.output.normal} "
        "--tsv-output {snakemake.output.tsv} "
        "--similar-removed {snakemake.output.removed_tsv} "
        "--removed-peptides {snakemake.output.removed_fasta} "
        " > {snakemake.output.tumor} "
        "{log}"
    )


.. |nl| raw:: html

   <br>