#!/opt/conda/conda-bld/deepvariant_1619786400309/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/bin/python
#
# Wrapper script for DeepVariant call_variants

BINARY_DIR="/opt/anaconda1anaconda2anaconda3/share/deepvariant-1.1.0-2/binaries/DeepVariant/1.1.0/DeepVariant-1.1.0"
MODEL_DIRS= {"wgs": "/opt/anaconda1anaconda2anaconda3/share/deepvariant-1.1.0-2/models/DeepVariant/1.1.0/DeepVariant-inception_v3-1.1.0+data-wgs_standard",
             "wes": "/opt/anaconda1anaconda2anaconda3/share/deepvariant-1.1.0-2/models/DeepVariant/1.1.0/DeepVariant-inception_v3-1.1.0+data-wes_standard",
             "pacbio": "/opt/anaconda1anaconda2anaconda3/share/deepvariant-1.1.0-2/models/DeepVariant/1.1.0/DeepVariant-inception_v3-1.1.0+data-pacbio_standard",
             "hybrid": "/opt/anaconda1anaconda2anaconda3/share/deepvariant-1.1.0-2/models/DeepVariant/1.1.0/DeepVariant-inception_v3-1.1.0+data-hybrid_standard"}

import argparse
import os
import subprocess
import sys

def real_dirname(path):
    """Return the symlink-resolved, canonicalized directory-portion of path."""
    return os.path.realpath(path)

class DVHelp(argparse._HelpAction):
    def __call__(self, parser, namespace, values, option_string=None):
        print("Baseline DeepVariant arguments")
        try:
            subprocess.check_output([sys.executable, "%s/call_variants.zip" % real_dirname(BINARY_DIR), "--help"])
        except subprocess.CalledProcessError as e:
            print(e.stdout.decode('UTF-8'))
        print()
        print("Wrapper arguments")
        parser.print_help()

def main():
    parser = argparse.ArgumentParser(description="DeepVariant call_variants wrapper", add_help=False)
    parser.add_argument("--cores", default=1)
    parser.add_argument("--outfile", required=True)
    parser.add_argument("--examples", required=True, help="Example directory from make_examples")
    parser.add_argument("--sample", required=True, help="Sample name")
    parser.add_argument("--model", default="wgs", choices=sorted(MODEL_DIRS.keys()),
                        help="DeepVariant trained model to use, defaults to wgs")
    parser.add_argument("-h", "--help", action=DVHelp)

    args = parser.parse_args()

    bin_dir = real_dirname(BINARY_DIR)
    model_dir = real_dirname(MODEL_DIRS[args.model])
    py_exe = sys.executable
    cmd = ("{py_exe} {bin_dir}/call_variants.zip "
           "--outfile {args.outfile} --examples {args.examples}/{args.sample}.tfrecord@{args.cores}.gz "
           "--checkpoint {model_dir}/model.ckpt")
    sys.exit(subprocess.call(cmd.format(**locals()), shell=True))

if __name__ == '__main__':
    main()
