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:

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:
        "0.72.0/bio/strling/extract"

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==0.3

Authors

  • Christopher Schröder

Code

"""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}"
)