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mmolarimmolari
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test: update input tree to the one generated by old treetime clock
this removes an extra single-child node, probably generated by the rust treetime clock command
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  • packages/treetime/src/commands/timetree/inference

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‎packages/treetime/src/commands/timetree/inference/runner.rs‎

Lines changed: 26 additions & 26 deletions
Original file line numberDiff line numberDiff line change
@@ -176,13 +176,14 @@ mod tests {
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// Rerooted H3N2 flu tree obtained from:
178178
//
179-
// cargo run --bin=treetime -- clock \
180-
// --tree data/flu/h3n2/20/tree.nwk \
181-
// --dates data/flu/h3n2/20/metadata.tsv \
182-
// --outdir tmp/clock_test
179+
// treetime clock \
180+
// --tree data/flu/h3n2/20/tree.nwk \
181+
// --dates data/flu/h3n2/20/metadata.tsv \
182+
// --sequence-length 1400 \
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// --outdir tmp/clock_test
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//
184-
// Output: tmp/clock_test/rerooted.nwk
185-
let input_nwk = r#"((A/Canterbury/58/2000|CY009150|09/05/2000|New_Zealand||H3N2/8-1416:0.00647,(A/New_York/182/2000|CY001279|02/18/2000|USA|99_00|H3N2/1-1409:0.0021,(A/Mexico/InDRE940/2003|CY100628|2003|Mexico||H3N2/15-1423:0.00578,(A/Managua/25/2007|CY032439|06/27/2007|Nicaragua||H3N2/1-1409:0.0035,(A/DaNang/DN434/2008|CY104616|11/11/2008|Viet_Nam||H3N2/4-1412:0.00428,(A/Boston/57/2008|CY044710|02/24/2008|USA|07_08|H3N2/1-1409:0.00214,((A/Oregon/15/2009|GQ895004|06/25/2009|USA|08_09|H3N2/1-1409:0.00214,A/Hong_Kong/H090_695_V10/2009|CY115546|07/10/2009|Hong_Kong||H3N2/8-1416:0.00357)NODE_0000006:0.00426,(A/Minab/797/2011|KC865620|12/24/2011|Iran||H3N2/20-1428:0.00761,(A/Peru/PER247/2011|CY162234|08/26/2011|Peru||H3N2/8-1416:0.00517,((A/Nebraska/15/2011|KC892583|12/15/2011|USA|11_12|H3N2/1-1409:0.00142,A/Maryland/21/2011|KC892695|12/26/2011|USA|11_12|H3N2/1-1409:0.00214)NODE_0000014:0.00214,(A/Indiana/03/2012|KC892731|04/03/2012|USA|11_12|H3N2/1-1409:0.00285,((A/Maryland/03/2013|KF789621|02/10/2013|USA|12_13|H3N2/1-1409:0.005,A/New_Hampshire/12/2012|KF790252|11/08/2012|USA|12_13|H3N2/1-1409:0.00071)NODE_0000015:0.00055,(A/Hawaii/02/2013|KF789866|05/28/2013|USA|12_13|H3N2/1-1409:0.00357,A/Boston/DOA2_107/2012|CY148382|11/01/2012|USA|12_13|H3N2/1-1409:0.00142)NODE_0000016:0.00055)NODE_0000000:0.00071)NODE_0000001:0.00286)NODE_0000002:0.00486)NODE_0000003:0.00184)NODE_0000004:0.00199)NODE_0000005:0.00074)NODE_0000007:0.00071)NODE_0000008:0.00055)NODE_0000009:0.0137)NODE_0000010:0.0101)NODE_0000011:0.00066)NODE_0000012:0.00393,((A/Scotland/76/2003|CY088128|11/03/2003|United_Kingdom|03_04|H3N2/1-1409:0.00143,A/Denmark/107/2003|EU103941|2003|Denmark||H3N2/1-1409:0.0007)NODE_0000013:0.0175):0.000437);"#;
185+
// Output: tmp/clock_test/rerooted.newick
186+
let input_nwk = r#"((A/Scotland/76/2003|CY088128|11/03/2003|United_Kingdom|03_04|H3N2/1-1409:0.00143,A/Denmark/107/2003|EU103941|2003|Denmark||H3N2/1-1409:0.00070)NODE_00000161.00:0.01778,(A/Canterbury/58/2000|CY009150|09/05/2000|New_Zealand||H3N2/8-1416:0.00647,(A/New_York/182/2000|CY001279|02/18/2000|USA|99_00|H3N2/1-1409:0.00210,(A/Mexico/InDRE940/2003|CY100628|2003|Mexico||H3N2/15-1423:0.00578,(A/Managua/25/2007|CY032439|06/27/2007|Nicaragua||H3N2/1-1409:0.00350,(A/DaNang/DN434/2008|CY104616|11/11/2008|Viet_Nam||H3N2/4-1412:0.00428,(A/Boston/57/2008|CY044710|02/24/2008|USA|07_08|H3N2/1-1409:0.00214,((A/Oregon/15/2009|GQ895004|06/25/2009|USA|08_09|H3N2/1-1409:0.00214,A/Hong_Kong/H090_695_V10/2009|CY115546|07/10/2009|Hong_Kong||H3N2/8-1416:0.00357)NODE_00000090.98:0.00426,(A/Minab/797/2011|KC865620|12/24/2011|Iran||H3N2/20-1428:0.00761,(A/Peru/PER247/2011|CY162234|08/26/2011|Peru||H3N2/8-1416:0.00517,((A/Nebraska/15/2011|KC892583|12/15/2011|USA|11_12|H3N2/1-1409:0.00142,A/Maryland/21/2011|KC892695|12/26/2011|USA|11_12|H3N2/1-1409:0.00214)NODE_00000050.93:0.00214,(A/Indiana/03/2012|KC892731|04/03/2012|USA|11_12|H3N2/1-1409:0.00285,((A/Maryland/03/2013|KF789621|02/10/2013|USA|12_13|H3N2/1-1409:0.00500,A/New_Hampshire/12/2012|KF790252|11/08/2012|USA|12_13|H3N2/1-1409:0.00071)NODE_00000010.47:0.00055,(A/Hawaii/02/2013|KF789866|05/28/2013|USA|12_13|H3N2/1-1409:0.00357,A/Boston/DOA2_107/2012|CY148382|11/01/2012|USA|12_13|H3N2/1-1409:0.00142)NODE_00000020.45:0.00055)NODE_0000000:0.00071)NODE_00000030.81:0.00286)NODE_00000040.96:0.00486)NODE_00000060.98:0.00184)NODE_00000070.79:0.00199)NODE_00000080.81:0.00074)NODE_00000100.81:0.00071)NODE_00000110.80:0.00055)NODE_00000120.87:0.01374)NODE_00000131.00:0.01010)NODE_00000141.00:0.00066)NODE_00000150.73:0.00408)NODE_0000017:0.00100;"#;
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187188
// From data/flu/h3n2/20/metadata.tsv
188189
let input_dates: DatesMap = btreemap! {
@@ -210,7 +211,7 @@ mod tests {
210211
// Python TreeTime v0 baseline results obtained from:
211212
//
212213
// treetime \
213-
// --tree tmp/clock_test/rerooted.nwk \
214+
// --tree tmp/clock_test/rerooted.newick \
214215
// --keep-root \
215216
// --clock-rate 0.0028 \
216217
// --dates data/flu/h3n2/20/metadata.tsv \
@@ -224,42 +225,41 @@ mod tests {
224225
// The --branch-length-mode input flag makes Python TreeTime use Poisson approximation
225226
// for branch length distributions (same as this test), enabling direct comparison.
226227
let expected = btreemap! {
227-
o!("NODE_0000017") => 1996.974064,
228-
o!("NODE_0000018") => 1997.116240,
229-
o!("NODE_0000012") => 1998.499705,
228+
o!("NODE_0000017") => 1996.895553,
229+
o!("NODE_00000161.00") => 2002.842738,
230+
o!("NODE_00000150.73") => 1998.478787,
230231
o!("A/Canterbury/58/2000|CY009150|09/05/2000|New_Zealand||H3N2/8-1416") => 2000.681725,
231-
o!("NODE_0000011") => 1998.763998,
232+
o!("NODE_00000141.00") => 1998.750301,
232233
o!("A/New_York/182/2000|CY001279|02/18/2000|USA|99_00|H3N2/1-1409") => 2000.134155,
233-
o!("NODE_0000010") => 2001.464619,
234+
o!("NODE_00000131.00") => 2001.455532,
234235
o!("A/Mexico/InDRE940/2003|CY100628|2003|Mexico||H3N2/15-1423") => 2003.002738,
235-
o!("NODE_0000009") => 2006.560498,
236+
o!("NODE_00000120.87") => 2006.561853,
236237
o!("A/Managua/25/2007|CY032439|06/27/2007|Nicaragua||H3N2/1-1409") => 2007.487337,
237-
o!("NODE_0000008") => 2006.896740,
238+
o!("NODE_00000110.80") => 2006.897741,
238239
o!("A/DaNang/DN434/2008|CY104616|11/11/2008|Viet_Nam||H3N2/4-1412") => 2008.865161,
239-
o!("NODE_0000007") => 2007.199495,
240+
o!("NODE_00000100.81") => 2007.200137,
240241
o!("A/Boston/57/2008|CY044710|02/24/2008|USA|07_08|H3N2/1-1409") => 2008.150582,
241-
o!("NODE_0000005") => 2007.458496,
242-
o!("NODE_0000006") => 2008.623669,
242+
o!("NODE_00000080.81") => 2007.459045,
243+
o!("NODE_00000090.98") => 2008.623974,
243244
o!("A/Oregon/15/2009|GQ895004|06/25/2009|USA|08_09|H3N2/1-1409") => 2009.481862,
244245
o!("A/Hong_Kong/H090_695_V10/2009|CY115546|07/10/2009|Hong_Kong||H3N2/8-1416") => 2009.522929,
245-
o!("NODE_0000004") => 2008.475043,
246+
o!("NODE_00000070.79") => 2008.475534,
246247
o!("A/Minab/797/2011|KC865620|12/24/2011|Iran||H3N2/20-1428") => 2011.980151,
247-
o!("NODE_0000003") => 2009.168874,
248+
o!("NODE_00000060.98") => 2009.169225,
248249
o!("A/Peru/PER247/2011|CY162234|08/26/2011|Peru||H3N2/8-1416") => 2011.651608,
249-
o!("NODE_0000002") => 2010.619876,
250-
o!("NODE_0000014") => 2011.351132,
250+
o!("NODE_00000040.96") => 2010.619950,
251+
o!("NODE_00000050.93") => 2011.351158,
251252
o!("A/Nebraska/15/2011|KC892583|12/15/2011|USA|11_12|H3N2/1-1409") => 2011.955510,
252253
o!("A/Maryland/21/2011|KC892695|12/26/2011|USA|11_12|H3N2/1-1409") => 2011.985626,
253-
o!("NODE_0000001") => 2011.528015,
254+
o!("NODE_00000030.81") => 2011.528039,
254255
o!("A/Indiana/03/2012|KC892731|04/03/2012|USA|11_12|H3N2/1-1409") => 2012.257358,
255-
o!("NODE_0000000") => 2011.869945,
256-
o!("NODE_0000015") => 2012.061411,
256+
o!("NODE_0000000") => 2011.869954,
257+
o!("NODE_00000010.47") => 2012.061416,
257258
o!("A/Maryland/03/2013|KF789621|02/10/2013|USA|12_13|H3N2/1-1409") => 2013.112252,
258259
o!("A/New_Hampshire/12/2012|KF790252|11/08/2012|USA|12_13|H3N2/1-1409") => 2012.856947,
259-
o!("NODE_0000016") => 2012.139149,
260+
o!("NODE_00000020.45") => 2012.139155,
260261
o!("A/Hawaii/02/2013|KF789866|05/28/2013|USA|12_13|H3N2/1-1409") => 2013.405202,
261262
o!("A/Boston/DOA2_107/2012|CY148382|11/01/2012|USA|12_13|H3N2/1-1409") => 2012.837782,
262-
o!("NODE_0000013") => 2002.842738,
263263
o!("A/Scotland/76/2003|CY088128|11/03/2003|United_Kingdom|03_04|H3N2/1-1409") => 2003.840520,
264264
o!("A/Denmark/107/2003|EU103941|2003|Denmark||H3N2/1-1409") => 2003.002738,
265265
};

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