INNER CODE UNIT · Python

combine_annotations

BortonWrightonLabs/DRAM · bin/combine_annotations.py:182

def combine_annotations(annotations_dir, genes_dir, dbcan_dir, output):
    """Combine annotation files with ranks and avoid duplicating specific columns."""
    annotations = sorted(Path(annotations_dir).glob("*")) if annotations_dir else []
    genes_faa = sorted(Path(genes_dir).glob("*")) if genes_dir else []
    dbcan_paths = (
        sorted(Path(dbcan_dir).glob("*dbCAN_hmm_results.tsv")) if dbcan_dir else []
    )
    dbcan_sub_paths = (
        sorted(Path(dbcan_dir).glob("*dbCANsub_hmm_results.tsv")) if dbcan_dir else []
    )
    annotation_frames = [
        frame
        for frame in (
            read_and_preprocess(path, input_fasta=input_fasta_from_filepath(path))
            for path in annotations
        )
        if frame is not None
    ]

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