GENEPREDTOBED

https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/ucsc/genePredToBed?label=version%20update%20pull%20requests

Convert from genePred to bed format. Does not yet handle genePredExt

URL: https://hgdownload.cse.ucsc.edu/admin/exe/

Example

This wrapper can be used in the following way:

rule test_genePredToBed:
    input:
        "annotation.genePred",
    output:
        "annotation.bed",
    params:
        extra="",
    log:
        "ucsc.log",
    wrapper:
        "v3.10.2-32-gf4e5b66/bio/ucsc/genePredToBed"

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

  • ucsc-genepredtobed=447

Input/Output

Input:

  • Path to a genePred file

Output:

  • Path to the output bed12 file

Params

  • extra: Optional parameters for genePredToBed

Authors

  • Thibault Dayris

Code

# coding: utf-8

__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=True, stderr=True)

shell("genePredToBed {extra} {snakemake.input} {snakemake.output} {log}")