[BioPython] downloading Genbank files continued
Ashleigh Smythe
absmythe at ucdavis.edu
Wed Apr 30 10:51:28 EDT 2003
Thanks for the comments. To clarify further...
1. I have downloaded sequences via the NCBI web interface for the
past few years but I'm doing bigger sets of taxa now and trying to
learn python/biopython so that's why I'm trying to learn this route
rather than my old web route.
2. I am trying to download gene sequences, not proteins.
3. As for the code I'm using I'm following the Genbank part of the
online tutorial from Bioinformatics.org, just trying it with a genus
that I know only has a few records:
>>>From Bio import GenBank
>>>gi_list=GenBank.search_for("Cervidellus")
Then to make sure I got something I do
>>>print gi_list
['16269590' , '6983954']
Then I create a dictionary
>>>ncbi_dict=GenBank.NCBIDictionary()
Then to fetch the records corresponding to my gi's
>>>gb_record=ncbi_dict[gi_list]
This chugs along fine, indicating what year it is searching, starting
in 2003, and then when it hits one of my records it gives me:
File ".../GenBank/__init__.py", line 1560, in __getitem__ raise
KeyError, "I unexpectedly got back html-formatted data."
4. This has failed each time for me but I've only tried a few taxa -
maybe I should try more.
I hope this clears things up a bit so maye someone can see what is going on.
Thanks again for the help!
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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