[Biopython] Fasta.index_file: functionality removed?
Cedar McKay
cmckay at u.washington.edu
Thu Jun 18 14:44:34 EDT 2009
On Jun 17, 2009, at 6:13 PM, Michiel de Hoon wrote:
> For the short term, the easiest solution for you is probably to pick
> up Bio.Fasta from an older version of Biopython. For the long term,
> it's probably best to integrate the indexing functionality in some
> way in Bio.SeqIO. Do you have some suggestions on how (from a user's
> perspective) this functionality should look like?
Ideally, it would look almost exactly like SeqIO.to_dict to the user,
except that instead of being in-memory it would transparently create
index files. Perhaps the user could pass optional parameters to
specify the name/location of the index file, and maybe another flag
could indicate whether the index files should persist, or are
automatically cleaned up when the user was finished and the dictionary-
like instance was destroyed.
best,
Cedar
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