.. _`bio/bellerophon`:

BELLEROPHON
===========


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

Filter mapped reads where the mapping spans a junction, retaining the 5-prime read.

**URL**: https://github.com/davebx/bellerophon/

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule bellerophon_sam:
        input:
            fwd="test_1500_forward.bam",
            rev="test_1500_reverse.bam",
        output:
            bam="out.sam",
        log:
            "logs/bellerophon.log",
        params:
            extra="--quality 20",
            sorting="none",  # optional: Enable sorting. Possible values: 'none', 'queryname' or 'coordinate'
            sort_extra="--no-PG",  # optional: extra arguments for samtools/picard
        threads: 2
        wrapper:
            "v3.0.1/bio/bellerophon"


    rule bellerophon_bam:
        input:
            fwd="test_1500_forward.bam",
            rev="test_1500_reverse.bam",
        output:
            bam="out.bam",
        log:
            "logs/bellerophon.log",
        params:
            extra="--quality 20",
            sorting="coordinate",  # optional: Enable sorting. Possible values: 'none', 'queryname' or 'coordinate'
            sort_extra="--no-PG",  # optional: extra arguments for samtools/picard
        threads: 2
        wrapper:
            "v3.0.1/bio/bellerophon"

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 `sort` param allows to enable sorting ('none', 'queryname' or 'coordinate').
* The `sort_extra` allows for extra arguments for samtools.
* The `extra` param allows for additional program arguments.


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

* ``bellerophon=1.0``
* ``samtools=1.18``
* ``snakemake-wrapper-utils=0.6.2``

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

* Forward reads (BAM format)
* Reverse reads (BAM format)

**Output:**

* SAM/BAM/CRAM file




Authors
-------

* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Filipe G. Vieira"
    __copyright__ = "Copyright 2022, Filipe G. Vieira"
    __license__ = "MIT"


    from snakemake.shell import shell
    from snakemake_wrapper_utils.samtools import get_samtools_opts


    samtools_opts = get_samtools_opts(snakemake, parse_output=False)
    log = snakemake.log_fmt_shell(stdout=False, stderr=True)
    extra = snakemake.params.get("extra", "")
    sort = snakemake.params.get("sorting", "none")
    sort_extra = snakemake.params.get("sort_extra", "")


    pipe_cmd = ""
    # Determine which pipe command to use for converting to bam or sorting.
    if sort == "none":
        # Simply convert to output format using samtools view.
        pipe_cmd = f"| samtools view -h {sort_extra} {samtools_opts}"
    elif sort in ["coordinate", "queryname"]:
        # Add name flag if needed.
        if sort == "queryname":
            sort_extra += " -n"

        # Sort alignments.
        pipe_cmd = f"| samtools sort {sort_extra} {samtools_opts}"
    else:
        raise ValueError(f"Unexpected value for params.sort: {sort}")


    shell(
        "(bellerophon"
        " --threads {snakemake.threads}"
        " --forward {snakemake.input.fwd}"
        " --reverse {snakemake.input.rev}"
        " {extra}"
        " --output /dev/stdout"
        " {pipe_cmd}"
        " > {snakemake.output[0]}"
        ") {log}"
    )


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