BEDGRAPHTOBIGWIG

Convert *.bedGraph file to *.bw file (see http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt)

Example

This wrapper can be used in the following way:

rule bedGraphToBigWig:
    input:
        bedGraph="{sample}.bedGraph",
        chromsizes="genome.chrom.sizes"
    output:
        "{sample}.bw"
    log:
        "logs/{sample}.bed-graph_to_big-wig.log"
    params:
        "" # optional params string
    wrapper:
        "v4.6.0-24-g250dd3e/bio/ucsc/bedGraphToBigWig"

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-bedgraphtobigwig=469

Input/Output

Input:

• bedGraph: Path to *.bedGraph file

• chromsizes: Chrom sizes file, could be generated by twoBitInfo or downloaded from UCSC

Output:

• Path to output ‘*.bw’ file

Authors

• Roman Cherniatchik

Code

"""Snakemake wrapper for *.bedGraph to *.bw conversion using UCSC bedGraphToBigWig tool."""

# http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt

__author__ = "Roman Chernyatchik"
__copyright__ = "Copyright (c) 2019 JetBrains"
__email__ = "roman.chernyatchik@jetbrains.com"
__license__ = "MIT"

from snakemake.shell import shell

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

shell(
    "bedGraphToBigWig {extra}"
    " {snakemake.input.bedGraph} {snakemake.input.chromsizes}"
    " {snakemake.output} {log}"
)