TRANSDECODER LONGORFS

TransDecoder.LongOrfs will identify coding regions within transcript sequences (ORFs) that are at least 100 amino acids long. You can lower this via the ‘-m’ parameter, but know that the rate of false positive ORF predictions increases drastically with shorter minimum length criteria.

Example

This wrapper can be used in the following way:

rule transdecoder_longorfs:
    input:
        fasta="test.fa.gz", # required
        gene_trans_map="test.gtm" # optional gene-to-transcript identifier mapping file (tab-delimited, gene_id<tab>trans_id<return> )
    output:
        "test.fa.transdecoder_dir/longest_orfs.pep"
    log:
        "logs/transdecoder/test-longorfs.log"
    params:
        extra=""
    wrapper:
        "v2.6.0-35-g755343f/bio/transdecoder/longorfs"

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

• transdecoder=5.7.1

Input/Output

Input:

• fasta transcripts

Output:

• ORFs peptide file(s)

Authors

• 14. Tessa Pierce

Code

"""Snakemake wrapper for Transdecoder LongOrfs"""

__author__ = "N. Tessa Pierce"
__copyright__ = "Copyright 2019, N. Tessa Pierce"
__email__ = "ntpierce@gmail.com"
__license__ = "MIT"

from os import path
from snakemake.shell import shell

extra = snakemake.params.get("extra", "")

log = snakemake.log_fmt_shell(stdout=True, stderr=True)

gtm_cmd = ""
gtm = snakemake.input.get("gene_trans_map", "")
if gtm:
    gtm_cmd = " --gene_trans_map " + gtm

output_dir = path.dirname(str(snakemake.output))

# transdecoder fails if output already exists. No force option available
shell("rm -rf {output_dir}")

input_fasta = str(snakemake.input.fasta)
if input_fasta.endswith("gz"):
    input_fa = input_fasta.rsplit(".gz")[0]
    shell("gunzip -c {input_fasta} > {input_fa}")
else:
    input_fa = input_fasta

shell("TransDecoder.LongOrfs -t {input_fa} {gtm_cmd} {log}")