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Add order, infraOrder, family to taxonomy blast output #513

Closed grace-ac closed 5 years ago

grace-ac commented 5 years ago

Currently, we get the genus and species, common name, and kingdom or domain names

-outfmt "6 qseqid sseqid evalue bitscore staxids sscinames scomnames sskingdoms" \

Would like to get some or all of these: order infraorder family

kubu4 commented 5 years ago

Does staxids provide more than one value? If yes, I believe each of those values (should be integers) indicate taxonomic lineage. You might be able to cross-reference those values with the NCBI taxonomy "dump"?

Edit: Embedded link didn't work. Here's the URL: ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump_readme.txt

sr320 commented 5 years ago

Go for it!

(See blastn -help)

Steven B. Roberts Kenneth K. Chew Endowed Professor School of Aquatic and Fishery Sciences University of Washington, Seattle WA sr320@uw.edu - 206.866.5141 robertslab.info - @sr320 On Dec 12, 2018, 12:55 PM -0800, grace-ac notifications@github.com, wrote:

Currently, we get the genus and species, common name, and kingdom or domain names -outfmt "6 qseqid sseqid evalue bitscore staxids sscinames scomnames sskingdoms" \ Would like to get some or all of these: order infraorder family — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.