Harrison Deng
18b003e0e2
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70 lines
1.9 KiB
Python
70 lines
1.9 KiB
Python
import argparse
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import asyncio
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import datetime
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from os import path
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import os
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from nsbdiagnosistoolkit.cli import aggregator
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from nsbdiagnosistoolkit.engine.data.genomics import NamedString
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from nsbdiagnosistoolkit.engine.local.abif import read_abif
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from nsbdiagnosistoolkit.engine.local.csv import write_mlst_profiles_as_csv
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from nsbdiagnosistoolkit.engine.local.fasta import read_fasta
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parser = argparse.ArgumentParser()
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parser.add_argument(
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"--run-name", "-name",
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dest="run_name",
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required=False,
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default=datetime.datetime.now().strftime(r"%Y%m%d%H%M%S"),
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type=str,
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help="The name of the run. Will use a date and time string if not provided."
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)
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parser.add_argument(
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"--fasta", "-fa", "-fst",
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nargs="+",
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action='extend',
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dest="fastas",
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required=False,
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default=[],
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type=str,
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help="The FASTA files to process. Multiple can be listed."
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)
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parser.add_argument(
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"--abif", "-abi", "-ab1",
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action='extend',
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dest="abifs",
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required=False,
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default=[],
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type=str,
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help="The ABIF files to process. Multiple can be listed."
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)
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parser.add_argument(
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"--institut-pasteur-mlst",
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"-ipdbmlst",
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dest="institut_pasteur_db",
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required=False,
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default=None,
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type=str,
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help="The Institut Pasteur MLST database to use."
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)
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parser.add_argument(
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"out",
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default="./.",
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help="The output folder. Files will be named by the provided (or default) run name."
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)
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def cli():
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args = parser.parse_args()
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gen_strings = aggregator.aggregate_sequences(args.fastas, args.abifs)
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os.makedirs(args.out, exist_ok=True)
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if args.institut_pasteur_db is not None:
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mlst_profiles = aggregator.profile_all_genetic_strings(
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gen_strings, args.institut_pasteur_db)
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asyncio.run(write_mlst_profiles_as_csv(
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asyncio.run(mlst_profiles), str(path.join(args.out, "MLST_" + args.run_name + ".csv"))))
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if __name__ == "__main__":
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cli() |