annotate ipapy2_MS2_annotation.py @ 0:cb18b8fcb441 draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a

from ipaPy2 import ipa
from utils import flattern_annotations, MSArgumentParser


def main(
    input_dataset_mapped_isotope_patterns,
    input_dataset_MS2,
    input_dataset_adducts,
    input_dataset_MS2_DB,
    ppm,
    ratiosd,
    ppmunk,
    ratiounk,
    ppmthr,
    pRTNone,
    pRTout,
    mzdCS,
    ppmCS,
    CSunk,
    evfilt,
    output_dataset,
    ncores,
):
    annotations = ipa.MSMSannotation(
        input_dataset_mapped_isotope_patterns,
        input_dataset_MS2,
        input_dataset_adducts,
        input_dataset_MS2_DB,
        ppm=ppm,
        ratiosd=ratiosd,
        ppmunk=ppmunk,
        ratiounk=ratiounk,
        ppmthr=ppmthr,
        pRTNone=pRTNone,
        pRTout=pRTout,
        mzdCS=mzdCS,
        ppmCS=ppmCS,
        CSunk=CSunk,
        evfilt=evfilt,
        ncores=ncores,
    )
    annotations_flat = flattern_annotations(annotations)
    write_func, file_path = output_dataset
    write_func(annotations_flat, file_path)


if __name__ == "__main__":
    parser = MSArgumentParser(
        """Annotation of the dataset base on the MS1 and MS2 information. Prior
    probabilities are based on mass only, while post probabilities are based
    on mass, RT, previous knowledge and isotope patterns."""
    )
    parser.add_argument(
        "--input_dataset_mapped_isotope_patterns",
        nargs=2,
        action="load_data",
        required=True,
        help=(
            "A dataset containing the MS1 data. Ideally obtained from"
            " map_isotope_patterns"
        ),
    )
    parser.add_argument(
        "--input_dataset_MS2",
        nargs=2,
        action="load_data",
        required=True,
        help="A dataset containing the MS2 fragmentation data",
    )
    parser.add_argument(
        "--input_dataset_adducts",
        nargs=2,
        action="load_data",
        required=True,
        help=(
            "A dataset containing the information on all the possible adducts given the"
            " database. Ideally obtained from compute_all_adducts"
        ),
    )
    parser.add_argument(
        "--input_dataset_MS2_DB",
        nargs=2,
        action="load_data",
        required=True,
        help="A dataset containing the MS2 database",
    )
    parser.add_argument(
        "--mzdCS",
        type=int,
        default=0,
        help="""maximum mz difference allowed when computing cosine similarity
           scores. If one wants to use this parameter instead of ppmCS, this
           must be set to 0. Default 0.""",
    )
    parser.add_argument(
        "--ppmCS",
        type=int,
        default=10,
        help="""maximum ppm allowed when computing cosine similarity scores.
           If one wants to use this parameter instead of mzdCS, this must be
           set to 0. Default 10.""",
    )
    parser.add_argument(
        "--CSunk",
        type=float,
        default=0.7,
        help="""cosine similarity score associated with the 'unknown' annotation.
            Default 0.7""",
    )
    parser.add_argument(
        "--evfilt",
        type=bool,
        default=False,
        help="""Default value False. If true, only spectrum acquired with the same
            collision energy are considered.""",
    )
    args = parser.parse_args()
    main(
        args.input_dataset_mapped_isotope_patterns,
        args.input_dataset_MS2,
        args.input_dataset_adducts,
        args.input_dataset_MS2_DB,
        args.ppm,
        args.ratiosd,
        args.ppmunk,
        args.ratiounk,
        args.ppmthr,
        args.pRTNone,
        args.pRTout,
        args.mzdCS,
        args.ppmCS,
        args.CSunk,
        args.evfilt,
        args.output_dataset,
        args.ncores,
    )