HMMPRESS

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

Format an HMM database into a binary format for hmmscan.

Example

This wrapper can be used in the following way:

rule hmmpress_profile:
    input:
        "test-profile.hmm"
    output:
        "test-profile.hmm.h3f",
        "test-profile.hmm.h3i",
        "test-profile.hmm.h3m",
        "test-profile.hmm.h3p"
    log:
        "logs/hmmpress.log"
    params:
        extra="",
    threads: 4
    wrapper:
        "v3.8.0-1-g149ef14/bio/hmmer/hmmpress"

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

  • hmmer=3.4

Input/Output

Input:

  • hmm database

Output:

  • binary format hmm database (for hmmscan)

Authors

  • N Tessa Pierce

Code

"""Snakemake wrapper for hmmpress"""

__author__ = "N. Tessa Pierce"
__copyright__ = "Copyright 2019, N. Tessa Pierce"
__email__ = "ntpierce@gmail.com"
__license__ = "MIT"

from os import path
from snakemake.shell import shell

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

# -f Force; overwrites any previous hmmpress-ed datafiles. The default is to bitch about any existing files and ask you to delete them first.

shell("hmmpress -f {snakemake.input} {log}")