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:
        "0.77.0-2-gf3a6529/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

Input/Output

Input:

  • GTF file

Output:

  • genePred table

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}")