.. _`bio/strling/extract`:

STRLING EXTRACT
===============


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

STRling (pronounced “sterling”) is a method to detect large short tandem repeat (STR) expansions from short-read sequencing data. ``extract`` retrieves informative read pairs to a binary format for a single sample (same as above, you can use the same bin files). Documentation at: https://strling.readthedocs.io/en/latest/run.html



Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule strling_extract:
        input:
            bam="mapped/{sample}.bam",
            bai="mapped/{sample}.bam.bai",
            reference="reference/genome.fasta",
            fai="reference/genome.fasta.fai",
            index="reference/genome.fasta.str" # optional
        output:
            "extract/{sample}.bin"
        log:
            "log/strling/extract/{sample}.log"
        params:
           extra="" # optionally add further command line arguments
        wrapper:
            "v3.0.1/bio/strling/extract"

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

* ``strling=0.5.2``




Authors
-------

* Christopher Schröder


Code
----

.. code-block:: python

    """Snakemake wrapper for strling extract"""

    __author__ = "Christopher Schröder"
    __copyright__ = "Copyright 2020, Christopher Schröder"
    __email__ = "christopher.schroede@tu-dortmund.de"
    __license__ = "MIT"

    from snakemake.shell import shell
    from os import path

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

    # Placeholder for optional parameters
    extra = snakemake.params.get("extra", "")

    # Check inputs/arguments.
    bam = snakemake.input.get("bam", None)
    reference = snakemake.input.get("reference", None)
    index = snakemake.input.get("index", None)

    if not bam or (isinstance(bam, list) and len(bam) != 1):
        raise ValueError("Please provide exactly one 'bam' input.")

    if not path.exists(bam + ".bai"):
        raise ValueError(
            "Please index the bam file. The index file must have same file name as the bam file, with '.bai' appended."
        )

    if not reference:
        raise ValueError("Please provide a fasta 'reference' input.")

    if not path.exists(reference + ".fai"):
        raise ValueError(
            "Please index the reference. The index file must have same file name as the reference file, with '.fai' appended."
        )

    if not index:  # optional
        index_string = ""
    else:
        index_string = "-g {}".format(index)

    if len(snakemake.output) != 1:
        raise ValueError("Please provide exactly one output file (.bin).")

    shell(
        "(strling extract "
        "{bam} "
        "{snakemake.output[0]} "
        "-f {reference} "
        "{index_string} "
        "{extra}) {log}"
    )


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