annotate pca.py @ 27:d37a7f17e35d draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5

import argparse

import numpy as np
from galaxy_ml.utils import read_columns
from sklearn.decomposition import IncrementalPCA, KernelPCA, PCA


def main():
    parser = argparse.ArgumentParser(description="RDKit screen")
    parser.add_argument("-i", "--infile", help="Input file")
    parser.add_argument(
        "--header", action="store_true", help="Include the header row or skip it"
    )
    parser.add_argument(
        "-c",
        "--columns",
        type=str.lower,
        default="all",
        choices=[
            "by_index_number",
            "all_but_by_index_number",
            "by_header_name",
            "all_but_by_header_name",
            "all_columns",
        ],
        help="Choose to select all columns, or exclude/include some",
    )
    parser.add_argument(
        "-ci",
        "--column_indices",
        type=str.lower,
        help="Choose to select all columns, or exclude/include some",
    )
    parser.add_argument(
        "-n",
        "--number",
        nargs="?",
        type=int,
        default=None,
        help="Number of components to keep. If not set, all components are kept",
    )
    parser.add_argument("--whiten", action="store_true", help="Whiten the components")
    parser.add_argument(
        "-t",
        "--pca_type",
        type=str.lower,
        default="classical",
        choices=["classical", "incremental", "kernel"],
        help="Choose which flavour of PCA to use",
    )
    parser.add_argument(
        "-s",
        "--svd_solver",
        type=str.lower,
        default="auto",
        choices=["auto", "full", "arpack", "randomized"],
        help="Choose the type of svd solver.",
    )
    parser.add_argument(
        "-b",
        "--batch_size",
        nargs="?",
        type=int,
        default=None,
        help="The number of samples to use for each batch",
    )
    parser.add_argument(
        "-k",
        "--kernel",
        type=str.lower,
        default="linear",
        choices=["linear", "poly", "rbf", "sigmoid", "cosine", "precomputed"],
        help="Choose the type of kernel.",
    )
    parser.add_argument(
        "-g",
        "--gamma",
        nargs="?",
        type=float,
        default=None,
        help="Kernel coefficient for rbf, poly and sigmoid kernels. Ignored by other kernels",
    )
    parser.add_argument(
        "-tol",
        "--tolerance",
        type=float,
        default=0.0,
        help="Convergence tolerance for arpack. If 0, optimal value will be chosen by arpack",
    )
    parser.add_argument(
        "-mi",
        "--max_iter",
        nargs="?",
        type=int,
        default=None,
        help="Maximum number of iterations for arpack",
    )
    parser.add_argument(
        "-d",
        "--degree",
        type=int,
        default=3,
        help="Degree for poly kernels. Ignored by other kernels",
    )
    parser.add_argument(
        "-cf",
        "--coef0",
        type=float,
        default=1.0,
        help="Independent term in poly and sigmoid kernels",
    )
    parser.add_argument(
        "-e",
        "--eigen_solver",
        type=str.lower,
        default="auto",
        choices=["auto", "dense", "arpack"],
        help="Choose the type of eigen solver.",
    )
    parser.add_argument(
        "-o", "--outfile", help="Base name for output file (no extension)."
    )
    args = parser.parse_args()

    usecols = None
    pca_params = {}

    if args.columns == "by_index_number" or args.columns == "all_but_by_index_number":
        usecols = [int(i) for i in args.column_indices.split(",")]
    elif args.columns == "by_header_name" or args.columns == "all_but_by_header_name":
        usecols = args.column_indices

    header = "infer" if args.header else None

    pca_input = read_columns(
        f=args.infile,
        c=usecols,
        c_option=args.columns,
        sep="\t",
        header=header,
        parse_dates=True,
        encoding=None,
        index_col=None,
    )

    pca_params.update({"n_components": args.number})

    if args.pca_type == "classical":
        pca_params.update({"svd_solver": args.svd_solver, "whiten": args.whiten})
        if args.svd_solver == "arpack":
            pca_params.update({"tol": args.tolerance})
        pca = PCA()

    elif args.pca_type == "incremental":
        pca_params.update({"batch_size": args.batch_size, "whiten": args.whiten})
        pca = IncrementalPCA()

    elif args.pca_type == "kernel":
        pca_params.update(
            {
                "kernel": args.kernel,
                "eigen_solver": args.eigen_solver,
                "gamma": args.gamma,
            }
        )

        if args.kernel == "poly":
            pca_params.update({"degree": args.degree, "coef0": args.coef0})
        elif args.kernel == "sigmoid":
            pca_params.update({"coef0": args.coef0})
        elif args.kernel == "precomputed":
            pca_input = np.dot(pca_input, pca_input.T)

        if args.eigen_solver == "arpack":
            pca_params.update({"tol": args.tolerance, "max_iter": args.max_iter})

        pca = KernelPCA()

    print(pca_params)
    pca.set_params(**pca_params)
    pca_output = pca.fit_transform(pca_input)
    np.savetxt(fname=args.outfile, X=pca_output, fmt="%.4f", delimiter="\t")


if __name__ == "__main__":
    main()