SEX.DETERRMINE

calculate the relative coverage of X and Y chromosomes, and their associated error bars, out of capture data.

Example

This wrapper can be used in the following way:

rule test_sexdeterrmine:
    input:
        depth="samples.depth.tsv",
    output:
        tsv="results.tsv",
        json="results.json",
    threads: 1
    log:
        "sexdeterrmine.log",
    wrapper:
        "v7.2.0/bio/sexdeterrmine"

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.

Notes

See depth header format at: https://github.com/TCLamnidis/Sex.DetERRmine/tree/master?tab=readme-ov-file#instructions

Software dependencies

• sexdeterrmine=1.1.2

Input/Output

Input:

• depth: Path to samtools depths file accross multiple samples with a header line giving sample names.

Output:

• Path to result table

Params

• No extra parameters handled.:

Authors

• Thibault Dayris

Code

# coding: utf-8

"""Snakemake wrapper for Sex.DetERRmine"""

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

from snakemake.shell import shell
from tempfile import TemporaryDirectory

import os
import os.path

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

with TemporaryDirectory() as tempdir:
    orig_path = os.path.realpath(os.getcwd())
    input_path = os.path.realpath(snakemake.input.depth)
    os.chdir(tempdir)
    commands = [
        f"sexdeterrmine --Input {input_path} {extra} > out.tsv",
    ]

    tsv = snakemake.output.get("tsv")
    if tsv:
        commands.append(f"mv --verbose out.tsv {orig_path}/{tsv}")

    json = snakemake.output.get("json")
    if json:
        commands.append(f"mv --verbose sexdeterrmine.json {orig_path}/{json}")

    commands = " && ".join(commands)
    shell("({commands}) {log}")