DEEPTOOLS COMPUTEMATRIX

deepTools computeMatrix calculates scores per genomic region. The matrix file can be used as input for other tools or for the generation of a deepTools plotHeatmap or deepTools plotProfiles. For usage information about deepTools computeMatrix, please see the documentation. For more information about deepTools, also see the source code.

computeMatrix option	Output format	Name of output variable to be used	Recommended extension
--outFileName, -out, -o	gzipped matrix file	matrix_gz (required)	“.gz”
--outFileNameMatrix	tab-separated table of matrix file	matrix_tab	“.tab”
--outFileSortedRegions	BED matrix file with sorted regions after skipping zeros or min/max threshold values	matrix_bed	“.bed”

URL: https://deeptools.readthedocs.io/en/develop/content/tools/computeMatrix.html

Example

This wrapper can be used in the following way:

rule compute_matrix:
    input:
        # Please note that the -R and -S options are defined via input files
        bed=expand("{sample}.bed", sample=["a", "b"]),
        bigwig=expand("{sample}.bw", sample=["a", "b"]),
        # Optional blacklist file
        # blacklist="",
    output:
        # Please note that --outFileName, --outFileNameMatrix and --outFileSortedRegions are exclusively defined via output files.
        # Usable output variables, their extensions and which option they implicitly call are listed here:
        #         https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/deeptools/computematrix.html.
        matrix_gz="matrix_files/matrix.gz",  # required
        # optional output files
        matrix_tab="matrix_files/matrix.tab",
        matrix_bed="matrix_files/matrix.bed",
    log:
        "logs/deeptools/compute_matrix.log",
    params:
        # required argument, choose "scale-regions" or "reference-point"
        command="scale-regions",
        # optional parameters
        extra="--regionBodyLength 200 --verbose",
    wrapper:
        "v5.8.0/bio/deeptools/computematrix"

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

[‘Bigwig DeepBlue URL, if any, should be given in params.extra, or downloaded separately.’]

Software dependencies

• deeptools=3.5.6

Input/Output

Input:

• bed: Path to BED or GTF files (.bed or .gtf) AND

• bigwig: Path to bigWig files (.bw)

Output:

• matrix_gz: gzipped matrix file (.gz) AND/OR

• matrix_tab: tab-separated table of matrix file (.tab) AND/OR

• matrix_bed: BED matrix file with sorted regions after skiping zeros or min/max threshold values (.bed)

Params

• command: Either scale-regions or reference-point

• extra: Optional parameters given to computeMatrix

Authors

• Antonie Vietor

• Thibault Dayris

Code

__author__ = "Antonie Vietor"
__copyright__ = "Copyright 2020, Antonie Vietor"
__email__ = "antonie.v@gmx.de"
__license__ = "MIT"

from snakemake.shell import shell
from tempfile import TemporaryDirectory

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

blacklist = snakemake.input.get("blacklist", "")
if blacklist:
    blacklist = f"--blackListFileName {blacklist}"

out_tab = snakemake.output.get("matrix_tab")
out_bed = snakemake.output.get("matrix_bed")

optional_output = ""

if out_tab:
    optional_output += " --outFileNameMatrix {out_tab} ".format(out_tab=out_tab)

if out_bed:
    optional_output += " --outFileSortedRegions {out_bed} ".format(out_bed=out_bed)


with TemporaryDirectory() as tempdir:
    temp = ""
    if "deepBlueURL" in snakemake.params.extra:
        temp = f"--deepBlueTempDir {tempdir}"

    shell(
        "computeMatrix "
        "{snakemake.params.command} "
        "{snakemake.params.extra} "
        "--numberOfProcessors {snakemake.threads} "
        "-R {snakemake.input.bed} "
        "-S {snakemake.input.bigwig} "
        "-o {snakemake.output.matrix_gz} "
        "{blacklist} {optional_output} {temp} {log}"
    )