INFER_EXPERIMENT

Report read strandiness and endeness

URL: https://rseqc.sourceforge.net/#infer-experiment-py

Example

This wrapper can be used in the following way:

rule test_rseqc_infer_experiment:
    input:
        aln="a.bam",
        refgene="genes.bed",
    output:
        "a.experiment.txt",
    log:
        "rseqc/infer_experiment.log",
    params:
        extra="-s 4 -q 3",
    wrapper:
        "v3.9.0/bio/rseqc/infer_experiment"

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

• rseqc=5.0.3

Input/Output

Input:

• aln: Path to SAM/BAM alignment file

• refgene: Path to reference gene model in bed format

Output:

• Path to text formated results

Params

• extra: Optional parameters for infer_experiment.py other than -i or -r

Authors

• Thibault Dayris

Code

# coding: utf-8

"""Snakemake wrapper for RSeQC infer experiment"""

__author__ = "Thibault Dayris"
__mail__ = "thibault.dayris@gustaveroussy.fr"
__copyright__ = "Copyright 2024, Thibault Dayris"
__license__ = "MIT"

from snakemake import shell

extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=False, stderr=True)

shell(
    "infer_experiment.py {extra} "
    "--input-file {snakemake.input.aln} "
    "--refgene {snakemake.input.refgene} "
    "> {snakemake.output} {log}"
)