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Frequency display defaults to genotypes

Modular augur build does not export clades into frequencies.json. This functionality could at some point be brought back, but in the interim, I've changed defaults to be genotype frequencies and also removed clades from options in the left hand text.
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trvrb committed Feb 12, 2019
1 parent 8b94548 commit 033ab98ba1e250a9b5d99599bf446e9c91d32375
Showing with 10 additions and 8 deletions.
  1. +6 −4 auspice/_layouts/auspice.html
  2. +4 −4 auspice/provision_directories.py
@@ -170,10 +170,12 @@ <h5 id="legend-title">Legend</h5>
</div>
</div>
<div class="spacer"></div>
Input mutations as position+amino acid, i.e. <span class="highlight">159Y</span>, clades as clade name,
i.e. <span class="highlight">3c2.a</span> and add locations as <span class="highlight">/AS</span>,
<span class="highlight">/NA</span>, <span class="highlight">/EU</span>, <span class="highlight">/OC</span>,
i.e. <span class="highlight">159Y/AS</span>. By default, positions are interpreted as residues in HA1. You can specify the subunit as <span class="highlight">HA2:18V</span>. Alternatively, simply click on variable positions in the graph below.
Input mutations as position+amino acid, i.e. <span class="highlight">159Y</span> and add
locations as <span class="highlight">/NA</span>, <span class="highlight">/EU</span>,
<span class="highlight">/OC</span>, i.e. <span class="highlight">159Y/AS</span>. By default,
positions are interpreted as residues in HA1. You can specify the subunit as
<span class="highlight">HA2:18V</span>. Alternatively, simply click on variable positions in
the graph below.
<div class="spacer"></div>
</div>
<div class="col-md-9">
@@ -30,10 +30,10 @@ def printdir():
}

virus_to_freqdefault = {
("H3N2", "HA"): "A1a, A1b, A2, A3, A4",
("H1N1pdm", "HA"): "6b.1, 6b.2, 164T",
("Vic", "HA"): "1A, 1B, 117V, DV",
("Yam", "HA"): "2, 3, 3a, 172Q",
("H3N2", "HA"): "HA1:135T, HA1:135K, HA1:135N, HA1:135A",
("H1N1pdm", "HA"): "HA1:183S, HA1:183P",
("Vic", "HA"): "HA1:129D, HA1:129N, HA1:129G, HA1:129S",
("Yam", "HA"): "HA1:229D, HA1:229N",
("H3N2", "NA"): "NA:161S, NA:329S, NA:220N",
("H1N1pdm", "NA"): "NA:446D, NA:44P",
("Vic", "NA"): "NA:220N, NA:371Q",

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