BUSCO¶
Assess assembly and annotation completeness with BUSCO
Software dependencies¶
- python ==3.6
- busco
Example¶
This wrapper can be used in the following way:
rule run_busco:
input:
"sample_data/target.fa"
output:
"txome_busco/full_table_txome_busco.tsv",
log:
"logs/quality/transcriptome_busco.log"
threads: 8
params:
mode="transcriptome",
lineage_path="sample_data/example",
# optional parameters
extra=""
wrapper:
"0.32.0/bio/busco"
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.
Authors¶
- Tessa Pierce
Code¶
"""Snakemake wrapper for BUSCO assessment"""
__author__ = "Tessa Pierce"
__copyright__ = "Copyright 2018, Tessa Pierce"
__email__ = "ntpierce@gmail.com"
__license__ = "MIT"
from snakemake.shell import shell
from os import path
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
extra = snakemake.params.get("extra", "")
mode = snakemake.params.get("mode")
assert mode is not None, "please input a run mode: genome, transcriptome or proteins"
lineage = snakemake.params.get("lineage_path")
assert lineage is not None, "please input the path to a lineage for busco assessment"
# busco does not allow you to direct output location: handle this by moving output
outdir = path.dirname(snakemake.output[0])
if '/' in outdir:
out_name = path.basename(outdir)
else:
out_name = outdir
#note: --force allows snakemake to handle rewriting files as necessary
# without needing to specify *all* busco outputs as snakemake outputs
shell("run_busco --in {snakemake.input} --out {out_name} --force "
" --cpu {snakemake.threads} --mode {mode} --lineage {lineage} "
" {extra} {log}" )
busco_outname = 'run_' + out_name
# move to intended location
shell("cp -r {busco_outname}/* {outdir}")
shell("rm -rf {busco_outname}")