[Biopython-dev] NCBI Abuse activity with Biopython

[Peter]

> As far as I can tell, Bio.GenBank is currently the only module in which
> Bio.EUtils is used, not counting modules that themselves have been
> deprecated. It shouldn't be too complicated to modify Bio.GenBank to use
> Bio.Entrez instead.

Looking back at CVS, it used to use Bio.WWW.NCBI once upon a time
(which is now Bio.Entrez), and had explicit rate limiting.  Then four
years ago Brad moved the Bio.GenBank.download_many() and search_for()
functions over to using Bio.EUtils (CVS revision 1.51 of
Bio/GenBank/__init__.py).

Brad also appears to have changed the functionality of
Bio.GenBank.download_many() from a call back mechanism to returning a
handle.  We could still return a handle, but it would require fetching
all the records (perhaps in batches), and concatenating them.  I think
it would make more sense to deprecate the Bio.GenBank.download_many()
function, and direct people to Bio.Entrez.efetch() instead.

The Bio.GenBank.search_for() still seems somewhat useful, but without
a default limit on the number of returned IDs, this could easily be
abused.  Again, we could deprecate this and direct people to
Bio.Entrez.esearch() instead.

Peter