.. _`bio/primerclip`:

PRIMERCLIP
==========


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

Primer trimming on sam file, https://github.com/swiftbiosciences/primerclip



Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule primerclip:
        input:
            v3.0.1_file="v3.0.1_file",
            alignment_file="mapped/{sample}.bam"
        output:
            alignment_file="mapped/{sample}.trimmed.bam"
        log:
            "logs/primerclip/{sample}.log"
        params:
            extra=""
        wrapper:
            "v3.0.1/bio/primerclip"

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

* ``samtools==1.9``
* ``primerclip==0.3.8``

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

* sam file
* master primer file

**Output:**

* sam file




Authors
-------

* Patrik Smeds


Code
----

.. code-block:: python

    __author__ = "Patrik Smeds"
    __copyright__ = "Copyright 2019, Patrik Smeds"
    __email__ = "patrik.smeds@gmail.com"
    __license__ = "MIT"


    from os import path

    from snakemake.shell import shell

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

    master_file = snakemake.input.master_file
    in_alignment_file = snakemake.input.alignment_file
    out_alignment_file = snakemake.output.alignment_file

    # Check inputs/arguments.
    if not isinstance(master_file, str):
        raise ValueError("master_file, path to the master file")

    if not isinstance(in_alignment_file, str):
        raise ValueError("in_alignment_file, path to the input alignment file")

    if not isinstance(out_alignment_file, str):
        raise ValueError("out_alignment_file, path to the output file")

    samtools_input_command = "samtools view -h " + in_alignment_file

    samtools_output_command = " | head -n -3 | samtools view -Sh"

    if out_alignment_file.endswith(".cram"):
        samtools_output_command += "C -o " + out_alignment_file
    elif out_alignment_file.endswith(".sam"):
        samtools_output_command += " -o " + out_alignment_file
    else:
        samtools_output_command += "b -o " + out_alignment_file

    shell(
        "{samtools_input_command} |"
        " primerclip"
        " {master_file}"
        " /dev/stdin"
        " /dev/stdout"
        " {samtools_output_command}"
        " {log}"
    )


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