PALADIN PREPARE

Download and prepare uniprot refs for paladin mapping. PALADIN is a protein sequence alignment tool designed for the accurate functional characterization of metagenomes.

Example

This wrapper can be used in the following way:

rule paladin_prepare:
    output:
        "uniprot_sprot.fasta.gz",
        "uniprot_sprot.fasta.gz.pro"
    log:
        "logs/paladin/prepare_sprot.log"
    params:
        reference_type=1, # 1=swiss-prot, 2=uniref90
    wrapper:
        "0.72.0/bio/paladin/prepare"

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

  • paladin=1.4.4
  • samtools=1.5

Authors

    1. Tessa Pierce

Code

"""Snakemake wrapper for Paladin Prepare"""

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

from snakemake.shell import shell

log = snakemake.log_fmt_shell(stdout=True, stderr=True)
extra = snakemake.params.get("extra", "")

reference_type = snakemake.params.get(
    "reference_type", "1"
)  # download swissprot as default
assert int(reference_type) in [1, 2]
ref_type_cmd = "-r" + str(reference_type)

shell("paladin prepare {ref_type_cmd} {extra} {log}")