genomic_pos_upload.py 文件源码

def get_ref_microbe_taxids():
        """
        Downloads the latest bacterial genome assembly summary from the NCBI genome
        ftp site and generate a list of taxids of the bacterial reference genomes.
        :return:
        """
        import urllib
        import csv

        urlbase = 'ftp://ftp.ncbi.nlm.nih.gov'
        urlextension = '/genomes/refseq/bacteria/assembly_summary.txt'
        assembly = urllib.urlopen(urlbase + urlextension)
        datareader = csv.reader(assembly.read().splitlines(), delimiter="\t")
        taxid = []

        for row in datareader:
            if row[4] == 'reference genome':
                taxid.append(row[5])

        ts = get_timestamp()
        dump(taxid, "ref_microbe_taxids_{}.pyobj".format(ts))

        return taxid