STRLING MERGE

STRling (pronounced “sterling”) is a method to detect large short tandem repeat (STR) expansions from short-read sequencing data. merge prepares joint calling of STR loci across all given samples. Requires minimum read evidence from at least one sample. Documentation at: https://strling.readthedocs.io/en/latest/run.html

Example

This wrapper can be used in the following way:

rule strling_merge:
    input:
        bins=["extract/A.bin", "extract/B.bin"],
        reference="reference/genome.fasta",
        fai="reference/genome.fasta.fai",
    output:
        "merged/group-bounds.txt" # must end with "-bounds.txt"
    params:
        extra="" # optionally add further command line arguments
    log:
        "log/strling/merge/group.log"
    wrapper:
        "v3.0.2-2-g0dea6a1/bio/strling/merge"

Note that input, output and log file paths can be chosen freely.

When running with

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

"""Snakemake wrapper for strling merge"""

__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.
bins = snakemake.input.get("bins", None)
reference = snakemake.input.get("reference", None)
fai = snakemake.input.get("fai", None)

if not bins or len(bins) < 2:
    raise ValueError("Please provide at least two 'bins' as input.")

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

if not snakemake.output[0].endswith("-bounds.txt"):
    raise ValueError(
        "Output file must end with '-bounds.txt'. Please change the output file name."
    )

prefix = snakemake.output[0][: -len("-bounds.txt")]

shell("(strling merge " "{bins} " "-o {prefix} " "{extra}) {log}")