PYROE ID-TO-NAME
Create a 2-column tab-separated file mapping IDs to names
URL: https://pyroe.readthedocs.io/en/latest/geneid_to_name.html
Example
This wrapper can be used in the following way:
rule test_pyroe_idtoname:
input:
"annotation.{format}",
output:
"id2name.{format}.tsv",
threads: 1
log:
"logs/{format}.log",
params:
extra="",
wrapper:
"v5.8.0/bio/pyroe/idtoname"
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.
Notes
Format is automatically inferred from input files.
Software dependencies
pyroe=0.9.3
Input/Output
Input:
Path to genome annotation (GTF or GFF3)
Output:
Path to gene id <-> gene names mapping
Params
extra
: Optional parameters to be passed to pyroe
Code
__author__ = "Thibault Dayris"
__copyright__ = "Copyright 2023, Thibault Dayris"
__email__ = "thibault.dayris@gustaveroussy.fr"
__license__ = "MIT"
from snakemake.shell import shell
log = snakemake.log_fmt_shell(stdout=True, stderr=True, append=True)
extra = snakemake.params.get("extra", "")
if str(snakemake.input).endswith(("gtf", "gtf.gz")):
extra += " --format GTF "
elif str(snakemake.input).endswith(("gff", "gff.gz", "gff3", "gff3.gz")):
extra += " --format GFF3 "
shell("pyroe id-to-name {extra} {snakemake.input} {snakemake.output} {log}")