run_prokka.py

import argparse
from multiprocessing import Pool
from pathlib import Path

from pyBioinfo_modules.basic.decompress import (getRootAndFiles,
                                                getStemIfCompressed)
from pyBioinfo_modules.bio_sequences.bio_seq_file_extensions import \
    FNA_EXTENSIONS
from pyBioinfo_modules.wrappers.prokka import runProkka

parser = argparse.ArgumentParser(description="Run prokka for fasta files")
parser.add_argument(
    "inputFiles",
    nargs="+",
    help="Input files/folders containing fasta files (can be gz or xz)",
)
parser.add_argument(
    "--parrllel", type=int, default=1, help="Number of prokka run in parallel"
)
parser.add_argument(
    "--threads",
    type=int,
    default=4,
    help="Number of threads for each prokka run",
)
parser.add_argument("--dry", action="store_true")

args = parser.parse_args()


outputRoot, targetFiles = getRootAndFiles(args.inputFiles, FNA_EXTENSIONS)

runnerPool = Pool(args.parrllel)
results = []
for f in targetFiles:
    prokkaDir = outputRoot / (getStemIfCompressed(f) + "_prokka")
    results.append(
        runnerPool.apply_async(
            runProkka,
            kwds={
                "fastaPath": f,
                "gcode": 11,
                "gram": "pos",
                "center": "MBT",
                "genus": None,
                "species": None,
                "strain": None,
                "locustag": None,
                "cpu": args.threads,
                "output": prokkaDir,
                "dry": args.dry,
                "silent": True,
            },
        )
    )

returns = []
for res in results:
    returns.append(res.get())