BioCompass.py 文件源码

def efetch_hit(term, seq_start, seq_stop):
    """ Fetch the relevant part of a hit
    """
    db = "nucleotide"

    maxtry = 3
    ntry = -1
    downloaded = False

    while ~downloaded and (ntry <= maxtry):
        ntry += 1
        try:
            handle = Entrez.esearch(db=db, term=term)
            record = Entrez.read(handle)

            assert len(record['IdList']) == 1, \
                    "Sorry, I'm not ready to handle more than one record"

            handle = Entrez.efetch(db=db, rettype="gb", retmode="text",
                    id=record['IdList'][0],
                    seq_start=seq_start, seq_stop=seq_stop)
            content = handle.read()
            downloaded = True
        except:
            nap = ntry*3
            print "Fail to download (term). I'll take a nap of %s seconds ", \
                    " and try again."
            time.sleep(ntry*3)

    return content