GTFTOGENEPRED¶
Convert a GTF file to genePred format (see https://genome.ucsc.edu/FAQ/FAQformat.html#format9)
URL:
Example¶
This wrapper can be used in the following way:
rule gtfToGenePred:
input:
# annotations containing gene, transcript, exon, etc. data in GTF format
"annotation.gtf"
output:
"annotation.genePred"
log:
"logs/gtfToGenePred.log"
params:
extra="-genePredExt" # optional parameters to pass to gtfToGenePred
wrapper:
"v1.2.0/bio/ucsc/gtfToGenePred"
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¶
ucsc-gtftogenepred==377
Authors¶
- Brett Copeland
Code¶
__author__ = "Brett Copeland"
__copyright__ = "Copyright 2021, Brett Copeland"
__email__ = "brcopeland@ucsd.edu"
__license__ = "MIT"
import os
from snakemake.shell import shell
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
shell("gtfToGenePred {extra} {snakemake.input} {snakemake.output} {log}")