DIAMOND BLASTX¶
DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data.
URL:
Example¶
This wrapper can be used in the following way:
rule diamond_blastx:
input:
fname_fastq = "{sample}.fastq",
fname_db = "db.dmnd"
output:
fname = "{sample}.tsv.gz"
log:
"logs/diamond_blastx/{sample}.log"
params:
extra="--header --compress 1"
threads: 8
wrapper:
"0.85.0/bio/diamond/blastx"
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¶
diamond==2.0.6
Authors¶
- Kim Philipp Jablonski
Code¶
__author__ = "Kim Philipp Jablonski"
__copyright__ = "Copyright 2020, Kim Philipp Jablonski"
__email__ = "kim.philipp.jablonski@gmail.com"
__license__ = "MIT"
from snakemake.shell import shell
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
shell(
"diamond blastx"
" --threads {snakemake.threads}"
" --db {snakemake.input.fname_db}"
" --query {snakemake.input.fname_fastq}"
" --out {snakemake.output.fname}"
" {extra}"
" {log}"
)