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:
        "v5.5.2-17-g33d5b76/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,
    append=False,
)
extra = snakemake.params.get("extra", "")

with TemporaryDirectory() as tempdir:
    old_path = os.getcwd()
    depth_path = os.path.realpath(snakemake.input.depth)
    os.chdir(tempdir)
    shell(f"sexdeterrmine --Input {depth_path} {extra} > out.tsv 2> sexdeterrmine.log")

    log = snakemake.log_fmt_shell(
        stdout=True,
        stderr=True,
        append=True,
    )

    os.chdir(old_path)
    os.replace(f"{tempdir}/sexdeterrmine.log", str(snakemake.log))

    tsv = snakemake.output.get("tsv")
    if tsv:
        shell("mv --verbose {tempdir}/out.tsv {tsv} {log}")

    json = snakemake.output.get("json")
    if json:
        shell("mv --verbose {tempdir}/sexdeterrmine.json {json} {log}")