gtm/lib/python3.12/site-packages/RUST/__main__.py

"""
script to run RUST as a cli tool 

Usage:
    RUST <command> [<args>...]

Options:
    -h --help   Show this screen.
    --version   Show version.


"""

import RUST

# import sys
# import time
# import traceback
import argparse


def parser():
    parser = argparse.ArgumentParser(description="RUST - Ribo-seq Unit Step Transform")
    parser.usage = "RUST <command> [<args>]"

    subparsers = parser.add_subparsers(help="mode of analysis")

    amino = subparsers.add_parser("amino", help="Run RUST on each amino acid")
    amino.add_argument(
        "-t",
        "--transcriptome",
        help="fasta file of transcripts, CDS start and end may be provided on description line using tab separation e.g. >NM_0001  10  5000, otherwise it searches for longest ORF"
        ", required=True",
    )
    amino.add_argument(
        "-a",
        "--alignment",
        help="sorted bam file of transcriptome alignments",
        required=True,
    )
    amino.add_argument("-o", "--offset", help="nucleotide offset to A-site", type=int)
    amino.add_argument(
        "-l",
        "--lengths",
        help="lengths of footprints included, for example 28:32 is 28,29,30,31,32",
    )
    amino.add_argument(
        "-P", "--Path", help='path to outputfile, default is "amino"', default="amino"
    )
    amino.set_defaults(mode="amino")

    codon = subparsers.add_parser("codon", help="Run RUST on each codon")
    codon.add_argument(
        "-t",
        "--transcriptome",
        help="fasta file of transcripts, CDS start and end may be provided on description line using tab separation e.g. >NM_0001  10  5000, otherwise it searches for longest ORF"
        ", required=True",
    )
    codon.add_argument(
        "-a",
        "--alignment",
        help="sorted bam file of transcriptome alignments",
        required=True,
    )
    codon.add_argument("-o", "--offset", help="nucleotide offset to A-site", type=int)
    codon.add_argument(
        "-l",
        "--lengths",
        help="lengths of footprints included, for example 28:32 is 28,29,30,31,32",
    )
    codon.add_argument(
        "-P", "--Path", help='path to outputfile, default is "codon"', default="codon"
    )
    codon.set_defaults(mode="codon")

    nucleotide = subparsers.add_parser("nucleotide", help="Run RUST on each nucleotide")
    nucleotide.add_argument(
        "-t",
        "--transcriptome",
        help="fasta file of transcripts, CDS start and end may be provided on description line using tab separation e.g. >NM_0001  10  5000, otherwise it searches for longest ORF"
        ", required=True",
    )
    nucleotide.add_argument(
        "-a",
        "--alignment",
        help="sorted bam file of transcriptome alignments",
        required=True,
    )
    nucleotide.add_argument(
        "-o", "--offset", help="nucleotide offset to A-site", type=int
    )
    nucleotide.add_argument(
        "-l",
        "--lengths",
        help="lengths of footprints included, for example 28:32 is 28,29,30,31,32",
    )
    nucleotide.add_argument(
        "-P",
        "--Path",
        help='path to outputfile, default is "nucleotide"',
        default="nucleotide",
    )
    nucleotide.set_defaults(mode="nucleotide")

    dipeptide = subparsers.add_parser("dipeptide", help="Run RUST on each dipeptide")
    dipeptide.add_argument(
        "-t",
        "--transcriptome",
        help="fasta file of transcripts, CDS start and end may be provided on description line using tab separation e.g. >NM_0001  10  5000, otherwise it searches for longest ORF"
        ", required=True",
    )
    dipeptide.add_argument(
        "-a",
        "--alignment",
        help="sorted bam file of transcriptome alignments",
        required=True,
    )
    dipeptide.add_argument(
        "-o", "--offset", help="nucleotide offset to A-site", type=int
    )
    dipeptide.add_argument(
        "-l",
        "--lengths",
        help="lengths of footprints included, for example 28:32 is 28,29,30,31,32",
    )
    dipeptide.add_argument(
        "-P",
        "--Path",
        help='path to outputfile, default is "dipeptide"',
        default="dipeptide",
    )
    dipeptide.set_defaults(mode="dipeptide")

    tripeptide = subparsers.add_parser("tripeptide", help="Run RUST on each tripeptide")
    tripeptide.add_argument(
        "-t",
        "--transcriptome",
        help="fasta file of transcripts, CDS start and end may be provided on description line using tab separation e.g. >NM_0001  10  5000, otherwise it searches for longest ORF"
        ", required=True",
    )
    tripeptide.add_argument(
        "-a",
        "--alignment",
        help="sorted bam file of transcriptome alignments",
        required=True,
    )
    tripeptide.add_argument(
        "-o", "--offset", help="nucleotide offset to A-site", type=int
    )
    tripeptide.add_argument(
        "-l",
        "--lengths",
        help="lengths of footprints included, for example 28:32 is 28,29,30,31,32",
    )
    tripeptide.add_argument(
        "-P",
        "--Path",
        help='path to outputfile, default is "tripeptide"',
        default="tripeptide",
    )
    tripeptide.set_defaults(mode="tripeptide")

    predict = subparsers.add_parser(
        "predict",
        help="Correlation between observed and predicted profiles from CDS start + 120 to CDS stop - 60",
    )
    predict.add_argument(
        "-t",
        "--transcriptome",
        help="fasta file of transcripts, CDS start and end may be provided on description line using tab separation e.g. >NM_0001  10  5000, otherwise it searches for longest ORF"
        ", required=True",
    )
    predict.add_argument(
        "-a",
        "--alignment",
        help="sorted bam file of transcriptome alignments",
        required=True,
    )
    predict.add_argument("-o", "--offset", help="nucleotide offset to A-site", type=int)
    predict.add_argument(
        "-l",
        "--lengths",
        help="lengths of footprints included, for example 28:32 is 28,29,30,31,32",
    )
    predict.add_argument(
        "-P",
        "--Path",
        help='path to outputfile, default is "amino"',
        default="predict_profiles",
    )
    predict.add_argument("-r", "--rustfile", help="path to rust file produced by codon")
    predict.add_argument(
        "-p",
        "--profiles",
        action="store_true",
        help="writes all profiles in csv files, may produce >10,000 files",
        default=False,
    )

    predict.set_defaults(mode="predict")

    synergy = subparsers.add_parser(
        "synergy",
        help="Identifies tripeptides that are candidates for synergistic interactions",
    )
    synergy.add_argument(
        "-t",
        "--transcriptome",
        help="fasta file of transcripts, CDS start and end may be provided on description line using tab separation e.g. >NM_0001  10  5000, otherwise it searches for longest ORF"
        ", required=True",
    )
    synergy.add_argument(
        "--aa", help='path to file produced from "rust_amino"', required=True
    )
    synergy.add_argument(
        "--tri", help='path to file produced from "rust_tripeptide"', required=True
    )
    synergy.add_argument(
        "-P",
        "--Path",
        help='path to outputfile, default is "synergy"',
        default="synergy",
    )
    synergy.set_defaults(mode="synergy")



    plot = subparsers.add_parser(
        "plot", help="Plot observed and predicted ribosome profiles"
    )
    plot.add_argument(
        "-t",
        "--transcriptome",
        help="fasta file of transcripts, CDS start and end may be provided on description line using tab separation e.g. >NM_0001  10  5000, otherwise it searches for longest ORF"
        ", required=True",
    )
    plot.add_argument(
        "-a",
        "--alignment",
        help="sorted bam file of transcriptome alignments",
        required=True,
    )
    plot.add_argument("-o", "--offset", help="nucleotide offset to A-site", type=int)
    plot.add_argument(
        "-l",
        "--lengths",
        help="lengths of footprints included, for example 28:32 is 28,29,30,31,32",
    )
    plot.add_argument(
        "-P", "--Path", help='path to outputfile, default is "amino"', default="plot"
    )
    plot.add_argument(
        "-i",
        "--identifier",
        help='Specific transcript to plot (Use of unique identifier is sufficient for example "NM_031946"',
        required=True,
    )
    plot.add_argument(
        "-r",
        "--rustfile",
        help='path to file produced from "rust_codon"',
        required=True,
    )
    plot.set_defaults(mode="plot")

    parser.add_argument("-v", "--version", action="version", version="%(prog)s 1.3.0")

    args = parser.parse_args()
    return args


def main():
    args = parser()

    if args.mode == "amino":
        RUST.amino.main(args)
        print(f"RUST successfully ran and outputted to {args.Path}")
    elif args.mode == "codon":
        RUST.codon.main(args)
        print(f"RUST successfully ran and outputted to {args.Path}")
    elif args.mode == "nucleotide":
        RUST.nucleotide.main(args)
        print(f"RUST successfully ran and outputted to {args.Path}")
    elif args.mode == "dipeptide":
        RUST.dipeptide.main(args)
        print(f"RUST successfully ran and outputted to {args.Path}")
    elif args.mode == "tripeptide":
        RUST.tripeptide.main(args)
        print(f"RUST successfully ran and outputted to {args.Path}")
    elif args.mode == "predict":
        RUST.predict_profiles.main(args)
        print(f"RUST successfully ran and outputted to {args.Path}")
    elif args.mode == "synergy":
        RUST.synergy.main(args)
        print(f"RUST successfully ran and outputted to {args.Path}")
    elif args.mode == "plot":
        RUST.plot_transcript.main(args)
        print(f"RUST successfully ran and outputted to {args.Path}")
    else:
        raise Exception(
            "Weird. RUST ran to end of program without triggering a pipeline or raising an error"
        )