ENSEMBL-ANNOTATION

Download annotation of genomic sites (e.g. transcripts) from ENSEMBL FTP servers, and store them in a single .gtf or .gff3 file.

Example

This wrapper can be used in the following way:

rule get_annotation:
    output:
        "refs/annotation.gtf"
    params:
        species="homo_sapiens",
        release="87",
        build="GRCh37",
        fmt="gtf",
        flavor="" # optional, e.g. chr_patch_hapl_scaff, see Ensembl FTP.
    log:
        "logs/get_annotation.log"
    cache: True  # save space and time with between workflow caching (see docs)
    wrapper:
        "0.72.0/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.

Software dependencies

  • curl

Authors

  • Johannes Köster

Code

__author__ = "Johannes Köster"
__copyright__ = "Copyright 2019, Johannes Köster"
__email__ = "johannes.koester@uni-due.de"
__license__ = "MIT"

import subprocess
import sys
from snakemake.shell import shell

species = snakemake.params.species.lower()
release = int(snakemake.params.release)
fmt = snakemake.params.fmt
build = snakemake.params.build
flavor = snakemake.params.get("flavor", "")

branch = ""
if release >= 81 and build == "GRCh37":
    # use the special grch37 branch for new releases
    branch = "grch37/"

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/{branch}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,
    branch=branch,
)

try:
    shell("(curl -L {url} | gzip -d > {snakemake.output[0]}) {log}")
except subprocess.CalledProcessError as e:
    if snakemake.log:
        sys.stderr = open(snakemake.log[0], "a")
    print(
        "Unable to download annotation data from Ensembl. "
        "Did you check that this combination of species, build, and release is actually provided?",
        file=sys.stderr,
    )
    exit(1)