MicrobeBotResources.py 文件源码

def get_microbe_taxids(force_download=False):
    """
    Download the latest bacterial genome assembly summary from the NCBI genome ftp site
    and generate a pd.DataFrame of relevant data for strain items based on taxids of the bacterial reference genomes.
    :return: pandas dataframe of bacteria reference genome data
    """
    if force_download or not os.path.exists("reference_genomes.csv"):
        assembly = urllib.request.urlretrieve("ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt")
        df = pd.read_csv(assembly[0], sep="\t", dtype=object, skiprows=1, header=0)
        df = df[df['refseq_category'].isin(['reference genome', 'representative genome'])]

        all_tax_wdid = id_mapper('P685')

        df['wdid'] = df['taxid'].apply(lambda x: all_tax_wdid.get(x, None))
        df = df.rename(columns={'# assembly_accession': 'assembly_accession'})
        df.to_csv('reference_genomes.csv', sep="\t")
        df.taxid = df.taxid.astype(int)
        return df
    else:  # use predownloaded and parsed flatfile
        df = pd.read_csv("reference_genomes.csv", sep="\t", dtype=object, index_col=0)
        df.taxid = df.taxid.astype(int)
        return df