kraken_trawl.py 文件源码

def add_isolates(dic_list, db_name):
    for assembly in dic_list:
        print("Adding {} to kraken stagging area.".format(assembly['organism']), file = sys.stderr)
        genbank_zip_file = assembly['dest']
        fi = gzip.open( genbank_zip_file, 'rt')
        seqs = list(SeqIO.parse( fi, 'genbank'))
        new_seqs = []
        for s in seqs:
            tmp = SeqIO.SeqRecord(s.seq)
            tmp.id = 'gi|{}'.format(s.annotations['gi'])
            tmp.description = s.description
            tmp.name = s.name
            new_seqs.append(tmp)
        fi.close()
        fa_file = os.path.join(os.getcwd(), os.path.basename(genbank_zip_file).strip('gbff.gz') + ".fa")
        tmpf = open(fa_file, 'wt')
        SeqIO.write(new_seqs, tmpf, 'fasta')
        tmpf.close()
        kraken_add(db_name, fa_file)
        # cmd = 'kraken-build --add-to-library {} --db {}'.format(fa_file, db_name)
        # print(cmd, file = sys.stderr)
        # cmd = shlex.split(cmd)
        # p = subprocess.check_output(cmd)
        # os.remove(fa_file)
    print("Added all {} assemblies to kraken stagging area. DB is ready to build".format(len(dic_list)), file = sys.stderr)

### ACTUALLY BUILD THE DATABASE ################################################