[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
says:
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.
Thanks!
Ashleigh
***************************
Ashleigh B. Smythe
Graduate Research Assistant
Department of Nematology
UC Davis
One Shield's Ave.
Davis, CA 95616
(530)754-4321
absmythe at ucdavis.edu
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