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fhcrc / taxtastic

Create and maintain phylogenetic "reference packages" of biological sequences.
GNU General Public License v3.0
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query ncbi entrez for accession tax_ids #68

Closed crosenth closed 8 years ago

crosenth commented 9 years ago
nhoffman commented 9 years ago

Chris - I hate to say it, but fetching taxids given a list of accessions NCBI seems like it should be implemented in a different subcommand - recall that the original description of this subcommand was "Look up a set of tax_ids from taxonomic names" using a local database. I could perhaps see adding an NCBI search for taxids given taxonomic names (ie, same functionality and output but make the local database optional), but taxids from accessions is a stretch. Keep in mind also that although we are only using NCBI for now, taxit could be generalized to use any taxononomy - an NCBI lookup breaks this generalization for this subcommand.

crosenth commented 9 years ago

Okay added a new subcommand entrez which does all the remote ncbi lookup stuff. Takes just accession numbers at the moment.