comparison customizemetadata.py @ 5:6dee4abadccb draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6

4:a16313517e55

    out_metadata = {
        'markers': in_metadata['markers'],
        'taxonomy': in_metadata['taxonomy'],
        'merged_taxon': {}
    }
    # transform merged_taxons tuple keys to string
    for k in in_metadata['merged_taxon']:
        n = ' , '.join(k)
        out_metadata[n] = in_metadata['merged_taxon'][k]

    }
    # transform merged_taxons keys to tuple
    for k in in_metadata['merged_taxon']:
        n = ' , '.split(k)
        out_metadata[n] = in_metadata['merged_taxon'][k]

    # dump metadata to Pickle file
    with bz2.BZ2File(pkl_fp, 'w') as pkl_f:
        pickle.dump(out_metadata, pkl_f)

5:6dee4abadccb

    out_metadata = {
        'markers': in_metadata['markers'],
        'taxonomy': in_metadata['taxonomy'],
        'merged_taxon': {}
    }

    # transform merged_taxons tuple keys to string
    for k in in_metadata['merged_taxon']:
        n = ' , '.join(k)
        out_metadata[n] = in_metadata['merged_taxon'][k]

    }
    # transform merged_taxons keys to tuple
    for k in in_metadata['merged_taxon']:
        n = ' , '.split(k)
        out_metadata[n] = in_metadata['merged_taxon'][k]

    # Ensure that there are 8 taxonomy levels (for compatibility between Metaphlan v3 and v4)
    # v3 DB release encodes the taxids as: ('2|1224|1236|91347|543|547|354276', 4404432)
    # v4 DB release encodes the taxids as: ('2|1224|1236|91347|543|547|354276|', 4404432)
    for k in out_metadata['taxonomy']:
        if out_metadata['taxonomy'][k][0].count('|') == 6:
            out_metadata['taxonomy'][k] = (out_metadata['taxonomy'][k][0] + '|', out_metadata['taxonomy'][k][1])

    # dump metadata to Pickle file
    with bz2.BZ2File(pkl_fp, 'w') as pkl_f:
        pickle.dump(out_metadata, pkl_f)