Download samples based on their ID from One Codex

download_ocx_samples.py

from __future__ import print_function
import argparse

import onecodex


if __name__ == "__main__":
    parser = argparse.ArgumentParser(
        description=("Download a set of FASTA/Q files stored in One Codex with their sample IDs."))
    parser.add_argument('samples', metavar='sample ID', nargs='+',
                        help='One Codex sample IDs to download')
    parser.add_argument('--api-key', default=None,
                        help='One Codex API key (optional if a ~/.onecodex file exists)')
    args = parser.parse_args()

    # Automatically fetch API key from ~/.onecodex file
    ocx = onecodex.Api(api_key=args.api_key)

    # Check that the verison is OK (> 0.2.0)
    assert tuple(int(x) for x in onecodex.version.__version__.split('.')) > (0, 2, 0)

    for ix, uuid in enumerate(args.samples):
        sample = ocx.Samples.get(uuid)
        if sample is None:
            raise Exception('Could not fetch sample {}. Double check that the Sample ID '
                            'is correct and that you are logged in with '
                            '`onecodex login`.'.format(uuid))
        print('Downloading {} (sample {}/{})...'.format(sample.filename, ix + 1, len(args.samples)))
        sample.download()

    print('Done!')