COMPLEMENTBED¶
Maps all regions of the genome which are not covered by the input.
URL: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html
Example¶
This wrapper can be used in the following way:
rule bedtools_complement_bed:
input:
in_file="a.bed",
genome="dummy.genome"
output:
"results/bed-complement/a.complement.bed"
params:
## Add optional parameters
extra="-L"
log:
"logs/a.complement.bed.log"
wrapper:
"v1.17.2/bio/bedtools/complement"
rule bedtools_complement_vcf:
input:
in_file="a.vcf",
genome="dummy.genome"
output:
"results/vcf-complement/a.complement.vcf"
params:
## Add optional parameters
extra="-L"
log:
"logs/a.complement.vcf.log"
wrapper:
"v1.17.2/bio/bedtools/complement"
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¶
bedtools=2.30
Authors¶
- Antonie Vietor
Code¶
__author__ = "Antonie Vietor"
__copyright__ = "Copyright 2020, Antonie Vietor"
__email__ = "antonie.v@gmx.de"
__license__ = "MIT"
from snakemake.shell import shell
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
shell(
"(bedtools complement"
" {extra}"
" -i {snakemake.input.in_file}"
" -g {snakemake.input.genome}"
" > {snakemake.output[0]})"
" {log}"
)