ENSEMBL-ANNOTATION¶
Download annotation of genomic sites (e.g. transcripts) from ENSEMBL FTP servers, and store them in a single .gtf or .gff3 file.
Software dependencies¶
- curl
Example¶
This wrapper can be used in the following way:
rule get_annotation:
output:
"refs/annotation.gtf"
params:
species="homo_sapiens",
release="98",
build="GRCh38",
fmt="gtf",
flavor="" # optional, e.g. chr_patch_hapl_scaff, see Ensembl FTP.
log:
"logs/get_annotation.log"
wrapper:
"0.50.4/bio/reference/ensembl-annotation"
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¶
- Johannes Köster
Code¶
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2019, Johannes Köster"
__email__ = "johannes.koester@uni-due.de"
__license__ = "MIT"
from snakemake.shell import shell
species = snakemake.params.species.lower()
release = snakemake.params.release
fmt = snakemake.params.fmt
build = snakemake.params.build
flavor = snakemake.params.get("flavor", "")
if flavor:
flavor += "."
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
suffix = ""
if fmt == "gtf":
suffix = "gtf.gz"
elif fmt == "gff3":
suffix = "gff3.gz"
url = "ftp://ftp.ensembl.org/pub/release-{release}/{fmt}/{species}/{species_cap}.{build}.{release}.{flavor}{suffix}".format(
release=release,
build=build,
species=species,
fmt=fmt,
species_cap=species.capitalize(),
suffix=suffix,
flavor=flavor,
)
shell("(curl -L {url} | gzip -d > {snakemake.output[0]}) {log}")