COOLTOOLS GENOME_BINNIFY

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Split chromosomes into equal sized bins

URL: https://github.com/open2c/cooltools

Example

This wrapper can be used in the following way:

rule cooltools_genome_binnify:
    input:
        chromsizes="hg38_chromsizes.txt",  ## Chromsizes file
    output:
        "hg38_1000000_bins.bed",
    params:
        binsize=1000000,
    threads: 1
    log:
        "logs/binnify.log",
    wrapper:
        "v3.10.2/bio/cooltools/genome/binnify"

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

  • cooltools=0.5.4

Input/Output

Input:

  • a chromsizes file

Output:

  • A .bed file with bin coordinates. Can have a {binsize} wildcard that specifies the resolution for the analysis, then it doesn’t need to be specified as a parameter.

Params

  • binsize: size of bins in bp. Optional, can be instead specified as a wildcard in the output

  • extra: Any additional arguments to pass

Authors

  • Ilya Flyamer

Code

__author__ = "Ilya Flyamer"
__copyright__ = "Copyright 2022, Ilya Flyamer"
__email__ = "flyamer@gmail.com"
__license__ = "MIT"

from snakemake.shell import shell

## Extract arguments
binsize = snakemake.params.get("binsize", snakemake.wildcards.get("binsize", 0))
if not binsize:
    raise ValueError("Please specify binsize either as a wildcard or as a parameter")

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


shell(
    "(cooltools genome binnify"
    " {snakemake.input.chromsizes} {binsize} "
    " {extra} "
    " > {snakemake.output}) {log}"
)