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Update download_all to work with segments #65

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trvrb opened this issue Jun 22, 2017 · 2 comments
Open

Update download_all to work with segments #65

trvrb opened this issue Jun 22, 2017 · 2 comments
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@huddlej

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@trvrb
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trvrb commented Jun 22, 2017

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.
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trvrb commented Jun 22, 2017

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"].

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ghost commented May 17, 2020

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

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