search

nextstrain / fauna

RethinkDB database to support real-time virus analysis
GNU Affero General Public License v3.0
33 stars 13 forks source link

Update download_all to work with segments #65

Open trvrb opened 7 years ago

trvrb commented 7 years ago

Current download_all.py writes sequences as h3n2.fasta etc... However, new augur wants h3n2_ha.fasta:

https://github.com/nextstrain/augur/tree/master/flu#how-to-run

The download_all.py script should be updated to download all segments and name them appropriately.

trvrb commented 7 years ago

Would also be good to add a --flu_segments command line option to mirror --flu_lineages. This should default to all 8 segments, like how --flu_lineages defaults to ["h3n2", "h1n1pdm", "vic", "yam"].

ghost commented 4 years ago

Hi @trvrb ! This issue is very old and had no interaction since 2017. Is it still a problem ?