.. _`bio/strling/call`:

STRLING CALL
============


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

STRling (pronounced like “sterling”) is a method to detect large short tandem repeat (STR) expansions from short-read sequencing data. ``call`` calls genotypes/estimate allele sizes for all loci in each sample. 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_call:
        input:
            bam="mapped/{sample}.bam",
            bai="mapped/{sample}.bam.bai",
            bin="extract/{sample}.bin",
            reference="reference/genome.fasta",
            fai="reference/genome.fasta.fai",
            bounds="merged/group-bounds.txt" # optional, produced by strling merge
        output:
            "call/{sample}-bounds.txt", # must end with -bounds.txt
            "call/{sample}-genotype.txt", # must end with -genotype.txt
            "call/{sample}-unplaced.txt" # must end with -unplaced.txt
        params:
            extra="" # optional extra command line arguments
        log:
            "log/strling/call/{sample}.log"
        wrapper:
            "v3.0.1/bio/strling/call"

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 call"""

    __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)
    bin = snakemake.input.get("bin", None)
    reference = snakemake.input.get("reference", None)
    bounds = snakemake.input.get("bounds", None)

    if not bam or (isinstance(bam, list) and len(bam) != 1):
        raise ValueError("Please provide exactly one 'bam' as 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 bounds:  # optional
        bounds_string = ""
    else:
        bounds_string = "-b {}".format(bounds)

    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 any(o.endswith("-bounds.txt") for o in snakemake.output):
        raise ValueError("Please provide a file that ends with -bounds.txt in the output.")

    for filename in snakemake.output:
        if filename.endswith("-bounds.txt"):
            prefix = filename[: -len("-bounds.txt")]
            break

    if not any(o == "{}-genotype.txt".format(prefix) for o in snakemake.output):
        raise ValueError(
            "Please provide an output file that ends with -genotype.txt and has the same prefix as -bounds.txt"
        )

    if not any(o == "{}-unplaced.txt".format(prefix) for o in snakemake.output):
        raise ValueError(
            "Please provide an output file that ends with -unplaced.txt and has the same prefix as -bounds.txt"
        )

    shell(
        "(strling call "
        "{bam} "
        "{bin} "
        "{bounds_string} "
        "-o {prefix} "
        "{extra}) {log}"
    )


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