HMMBUILD

hmmbuild: construct profile HMM(s) from multiple sequence alignment(s)

URL:

Example

This wrapper can be used in the following way:

rule hmmbuild_profile:
    input:
        "test-profile.sto"
    output:
        "test-profile.hmm"
    log:
        "logs/test-profile-hmmbuild.log"
    params:
        extra="",
    threads: 4
    wrapper:
        "v1.2.1/bio/hmmer/hmmbuild"

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=3.2.1

Input/Output

Input:

  • sequence alignment file

Output:

  • profile hmm

Authors

  • N Tessa Pierce

Code

"""Snakemake wrapper for hmmbuild"""

__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

extra = snakemake.params.get("extra", "")

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

shell(
    " hmmbuild {extra} --cpu {snakemake.threads} "
    " {snakemake.output} {snakemake.input} {log} "
)