[Biopython-dev] NCBI Abuse activity with Biopython

Peter biopython at maubp.freeserve.co.uk
Thu Jun 26 14:43:10 UTC 2008

OK then - I will deprecate the Bio.GenBank.search_for() and
Bio.GenBank,download_many() functions, suggesting Bio.Entrez instead.
I will also update the tutorial on this.

On Thu, Jun 26, 2008 at 2:51 PM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> Btw, NCBIDictionary definitely needs to go.
> From the documentation, continuing the example above:
>>>> ncbi_dict = GenBank.NCBIDictionary("nucleotide", "genbank")
>>>> gb_record = ncbi_dict[gi_list[0]]
> Hence, we're running efetch once for each key separately; this is exactly what NCBI advised against.

If the user wants to run a Entrez search and then fetch some/all of
the results, then yes, the NCBI would not want us to do a multiple
separate efetch calls by idenifier.  Could you prepare an example
using Bio.Entrez with the "history" (WebEnv argument)?

However, if the user has provided the list of GI numbers (e.g. from a
file), there is no existing NCBI search data to refer to, and I don't
see any other option.  So there is a use-case for the
Bio.GenBank.NCBIDictionary class.


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