pipeline.py 文件源码

def sample_to_metadata_mapping(samples_dir):
    '''
    return dict
    each key is string "sample_id"
    each value is a list of metadata ordered as
    ["strain", "sample_id", "collect_date", "country", "division", "location"]
    '''
    metadata_file = samples_dir + "samples.tsv"
    sm_mapping = {}
    with open(metadata_file) as tsv:
        for row in csv.DictReader(tsv, delimiter="\t"):
            sample = row["sample_id"]
            metadata = [row["strain"], row["sample_id"], row["collection_date"],
                row["country"], row["division"], row["location"]]
            sm_mapping[sample] = metadata
    return sm_mapping