[BioPython] downloading Genbank files from NCBI

Ashleigh Smythe absmythe at ucdavis.edu
Tue Apr 29 19:28:48 EDT 2003

Hello.  I've been learning to use python and biopython for a few 
months now but am also new to programming/Linux in general so please 
forgive me for being slow!

I want to use biopython to download files of certain taxa and certain 
genes from Genbank.  I've been following the tutorial on the 
biopython website. I can use the search_for attribute from the 
GenBank module to get identifiers for sequence records but when I try 
to use GenBank.NCBIDictionary() to actually get the records it chugs 
along fine until it finds the record and then I get an error that 

File ".../GenBank/__init__.py", line 1560, in __getitem__ raise 
KeyError, "I unexpectedly got back html-formatted data."

I don't know to fix the NCBIDictionary code to fix this.  I have been 
trying various other ways in general to extract the records I want 
from Genbank, such as parsing the big flat files but I haven't yet 
figured out how to extract the records I want.

Any suggestions as to how to fix the NCBIDictionary problem or how to 
do what I want to do in some other way would be greatly appreciated.

Ashleigh B. Smythe
Graduate Research Assistant
Department of Nematology
UC Davis
One Shield's Ave.
Davis, CA 95616
absmythe at ucdavis.edu

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