[Biopython] NCBIWWW genbank files

[Ara Kooser]

Good morning all,


   I am in the process of writing some code for pulling down files from NCBI. I wrote this based on the Biopython manual:

from Bio.Blast import NCBIWWW

def query():
    file_query = raw_input("Please enter the name of your sequence file: ")
    fasta_seq = open(file_query).read()
    result_handle = NCBIWWW.qblast("blastn","nr", fasta_seq, expect=1e-30, hitlist_size=20000)
    save_file = open("blast_results.xml","w")
    save_file.write(result_handle.read())
    save_file.close()
    result_handle.close()


query()

Everything works fine. But I was wondering is there a way to pull down the Genbank files using this method. I used the help(NCBIWWW.qblast) to look at all the options but didn't see the Genbank file format. Downstream in the program I use information extracted from both the .xml and genbank files since they contain different information to we need. I was hoping to combine everything into one program. Currently we use the web interface to pull down the xml and genbank files.

Thanks!
Ara