[Biopython] Needs some NCBI recommendation

lueck at ipk-gatersleben.de lueck at ipk-gatersleben.de
Sun Jan 3 11:19:50 UTC 2010


Hello and a happy new year!

I'm currently writing a small software, which allows the users to 
perform a NCBI online BLAST and to download full records from NCBI via 
PubMed IDs in a batch mode.

I would like to limit the BLAST and Download, in order not to abuse 
NCBI. What would you suggest for an input limitation for BLAST and 
Sequence Download (using efetch)?

In addition I want to ask, whether it's reasonable to use the efecth in 
a simple for statement

id_list = ["19304878", "18606172"]
for i in id_list:
    handle = Entrez.efetch(db="nucleotide", id=i, rettype="fasta")
    print handle.read()

since I need only the raw GenBank or FASTA files?

Thanks for any advice!
Stefanie




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