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:
"v1.15.1/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}"
)