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update based on latest constellations
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@rmcolq
rmcolq committed Aug 21, 2023
1 parent 122ff5e commit 4b81c92
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Showing 4 changed files with 61 additions and 61 deletions.
2 changes: 1 addition & 1 deletion scorpio/tests/data/classify/expected.multi_list_incompatible_long.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ Flatland/P.3/2021,,,,,,,,,,,
Flatland/B.1.525/2020,,,,,,,,,,,
Flatland/P.2/2021,Zeta (P.2-like),P.2,,1,6,0,0,2,0.857100,0.142900,Zeta (P.2-like)
Flatland/C.37/2021,,,,,,,,,,,
Flatland/BA.1/2022,Omicron (BA.1-like),BA.1,,0,55,1,3,5,0.932200,0.000000,Omicron (BA.1-like)
Flatland/BA.1/2022,Omicron (BA.1-like),BA.1,,0,54,1,3,5,0.931000,0.000000,Omicron (BA.1-like)
Flatland/BA.2/2022,,,,,,,,,,,
Flatland/BA.3/2022,,,,,,,,,,,
Flatland/XE/2022,,,,,,,,,,,
40 changes: 20 additions & 20 deletions scorpio/tests/data/classify/expected.multi_output_counts_classify.Omicron__BA.1-like_.csv
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@@ -1,21 +1,21 @@
query,ref_count,alt_count,ambig_count,other_count,rule_count,support,conflict,call,constellation_name,note
Flatland/B.1.1.7/2021,48,8,0,3,1,0.135600,0.813600,False,Omicron (BA.1-like),
Flatland/B.1.351/2021,44,5,9,1,1,0.084700,0.745800,False,Omicron (BA.1-like),
Flatland/P.1/2021,49,7,0,3,1,0.118600,0.830500,False,Omicron (BA.1-like),
Flatland/P.1_again/2021,49,7,0,3,1,0.118600,0.830500,False,Omicron (BA.1-like),
Flatland/B.1.617.1/2021,48,4,2,5,1,0.067800,0.813600,False,Omicron (BA.1-like),
Flatland/B.1.617.2/2021,48,6,0,5,1,0.101700,0.813600,False,Omicron (BA.1-like),
Flatland/B.1.617.2_K417N/2021,46,6,0,7,1,0.101700,0.779700,False,Omicron (BA.1-like),
Flatland/AY.4/2021,47,7,0,5,1,0.118600,0.796600,False,Omicron (BA.1-like),
Flatland/AY.4.2/2021,46,7,1,5,1,0.118600,0.779700,False,Omicron (BA.1-like),
Flatland/B.1.427/2021,54,4,0,1,1,0.067800,0.915300,False,Omicron (BA.1-like),
Flatland/B.1.429/2021,55,3,0,1,1,0.050800,0.932200,False,Omicron (BA.1-like),
Flatland/B.1.526/2021,50,7,0,2,1,0.118600,0.847500,False,Omicron (BA.1-like),
Flatland/P.3/2021,47,7,0,5,1,0.118600,0.796600,False,Omicron (BA.1-like),
Flatland/B.1.525/2020,50,5,0,4,1,0.084700,0.847500,False,Omicron (BA.1-like),
Flatland/P.2/2021,52,4,0,3,1,0.067800,0.881400,False,Omicron (BA.1-like),
Flatland/C.37/2021,50,8,0,1,1,0.135600,0.847500,False,Omicron (BA.1-like),
Flatland/BA.1/2022,0,55,1,3,5,0.932200,0.000000,default,Omicron (BA.1-like),
Flatland/BA.2/2022,18,38,0,3,3,0.644100,0.305100,False,Omicron (BA.1-like),
Flatland/BA.3/2022,14,28,15,2,2,0.474600,0.237300,False,Omicron (BA.1-like),
Flatland/XE/2022,14,42,0,3,3,0.711900,0.237300,False,Omicron (BA.1-like),
Flatland/B.1.1.7/2021,47,8,0,3,1,0.137900,0.810300,False,Omicron (BA.1-like),
Flatland/B.1.351/2021,44,4,9,1,1,0.069000,0.758600,False,Omicron (BA.1-like),
Flatland/P.1/2021,49,7,0,2,1,0.120700,0.844800,False,Omicron (BA.1-like),
Flatland/P.1_again/2021,49,7,0,2,1,0.120700,0.844800,False,Omicron (BA.1-like),
Flatland/B.1.617.1/2021,47,4,2,5,1,0.069000,0.810300,False,Omicron (BA.1-like),
Flatland/B.1.617.2/2021,47,6,0,5,1,0.103400,0.810300,False,Omicron (BA.1-like),
Flatland/B.1.617.2_K417N/2021,46,5,0,7,1,0.086200,0.793100,False,Omicron (BA.1-like),
Flatland/AY.4/2021,46,7,0,5,1,0.120700,0.793100,False,Omicron (BA.1-like),
Flatland/AY.4.2/2021,45,7,1,5,1,0.120700,0.775900,False,Omicron (BA.1-like),
Flatland/B.1.427/2021,53,4,0,1,1,0.069000,0.913800,False,Omicron (BA.1-like),
Flatland/B.1.429/2021,54,3,0,1,1,0.051700,0.931000,False,Omicron (BA.1-like),
Flatland/B.1.526/2021,49,7,0,2,1,0.120700,0.844800,False,Omicron (BA.1-like),
Flatland/P.3/2021,46,7,0,5,1,0.120700,0.793100,False,Omicron (BA.1-like),
Flatland/B.1.525/2020,49,5,0,4,1,0.086200,0.844800,False,Omicron (BA.1-like),
Flatland/P.2/2021,51,4,0,3,1,0.069000,0.879300,False,Omicron (BA.1-like),
Flatland/C.37/2021,49,8,0,1,1,0.137900,0.844800,False,Omicron (BA.1-like),
Flatland/BA.1/2022,0,54,1,3,5,0.931000,0.000000,default,Omicron (BA.1-like),
Flatland/BA.2/2022,18,37,0,3,3,0.637900,0.310300,False,Omicron (BA.1-like),
Flatland/BA.3/2022,14,28,14,2,2,0.482800,0.241400,False,Omicron (BA.1-like),
Flatland/XE/2022,14,41,0,3,3,0.706900,0.241400,False,Omicron (BA.1-like),
40 changes: 20 additions & 20 deletions scorpio/tests/data/classify/expected.single_mutations_output_counts_classify.csv
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Original file line number Diff line number Diff line change
@@ -1,21 +1,21 @@
query,constellations,mrca_lineage,ref_count,alt_count,ambig_count,other_count,rule_count,support,conflict,constellation_name,call,note,ORF3a:S26L,nuc:T17040C
Flatland/B.1.1.7/2021,48,8,0,3,1,0.135600,0.813600,False,Omicron (BA.1-like),,S,T
Flatland/B.1.351/2021,44,5,9,1,1,0.084700,0.745800,False,Omicron (BA.1-like),,S,T
Flatland/P.1/2021,49,7,0,3,1,0.118600,0.830500,False,Omicron (BA.1-like),,S,T
Flatland/P.1_again/2021,49,7,0,3,1,0.118600,0.830500,False,Omicron (BA.1-like),,S,T
Flatland/B.1.617.1/2021,48,4,2,5,1,0.067800,0.813600,False,Omicron (BA.1-like),,L,T
Flatland/B.1.617.2/2021,48,6,0,5,1,0.101700,0.813600,False,Omicron (BA.1-like),,L,T
Flatland/B.1.617.2_K417N/2021,46,6,0,7,1,0.101700,0.779700,False,Omicron (BA.1-like),,L,T
Flatland/AY.4/2021,47,7,0,5,1,0.118600,0.796600,False,Omicron (BA.1-like),,L,C
Flatland/AY.4.2/2021,46,7,1,5,1,0.118600,0.779700,False,Omicron (BA.1-like),,L,C
Flatland/B.1.427/2021,54,4,0,1,1,0.067800,0.915300,False,Omicron (BA.1-like),,S,T
Flatland/B.1.429/2021,55,3,0,1,1,0.050800,0.932200,False,Omicron (BA.1-like),,S,T
Flatland/B.1.526/2021,50,7,0,2,1,0.118600,0.847500,False,Omicron (BA.1-like),,S,T
Flatland/P.3/2021,47,7,0,5,1,0.118600,0.796600,False,Omicron (BA.1-like),,S,T
Flatland/B.1.525/2020,50,5,0,4,1,0.084700,0.847500,False,Omicron (BA.1-like),,S,T
Flatland/P.2/2021,52,4,0,3,1,0.067800,0.881400,False,Omicron (BA.1-like),,S,T
Flatland/C.37/2021,50,8,0,1,1,0.135600,0.847500,False,Omicron (BA.1-like),,S,T
Flatland/BA.1/2022,0,55,1,3,5,0.932200,0.000000,default,Omicron (BA.1-like),,S,T
Flatland/BA.2/2022,18,38,0,3,3,0.644100,0.305100,False,Omicron (BA.1-like),,S,T
Flatland/BA.3/2022,14,28,15,2,2,0.474600,0.237300,False,Omicron (BA.1-like),,S,T
Flatland/XE/2022,14,42,0,3,3,0.711900,0.237300,False,Omicron (BA.1-like),,S,T
Flatland/B.1.1.7/2021,47,8,0,3,1,0.137900,0.810300,False,Omicron (BA.1-like),,S,T
Flatland/B.1.351/2021,44,4,9,1,1,0.069000,0.758600,False,Omicron (BA.1-like),,S,T
Flatland/P.1/2021,49,7,0,2,1,0.120700,0.844800,False,Omicron (BA.1-like),,S,T
Flatland/P.1_again/2021,49,7,0,2,1,0.120700,0.844800,False,Omicron (BA.1-like),,S,T
Flatland/B.1.617.1/2021,47,4,2,5,1,0.069000,0.810300,False,Omicron (BA.1-like),,L,T
Flatland/B.1.617.2/2021,47,6,0,5,1,0.103400,0.810300,False,Omicron (BA.1-like),,L,T
Flatland/B.1.617.2_K417N/2021,46,5,0,7,1,0.086200,0.793100,False,Omicron (BA.1-like),,L,T
Flatland/AY.4/2021,46,7,0,5,1,0.120700,0.793100,False,Omicron (BA.1-like),,L,C
Flatland/AY.4.2/2021,45,7,1,5,1,0.120700,0.775900,False,Omicron (BA.1-like),,L,C
Flatland/B.1.427/2021,53,4,0,1,1,0.069000,0.913800,False,Omicron (BA.1-like),,S,T
Flatland/B.1.429/2021,54,3,0,1,1,0.051700,0.931000,False,Omicron (BA.1-like),,S,T
Flatland/B.1.526/2021,49,7,0,2,1,0.120700,0.844800,False,Omicron (BA.1-like),,S,T
Flatland/P.3/2021,46,7,0,5,1,0.120700,0.793100,False,Omicron (BA.1-like),,S,T
Flatland/B.1.525/2020,49,5,0,4,1,0.086200,0.844800,False,Omicron (BA.1-like),,S,T
Flatland/P.2/2021,51,4,0,3,1,0.069000,0.879300,False,Omicron (BA.1-like),,S,T
Flatland/C.37/2021,49,8,0,1,1,0.137900,0.844800,False,Omicron (BA.1-like),,S,T
Flatland/BA.1/2022,0,54,1,3,5,0.931000,0.000000,default,Omicron (BA.1-like),,S,T
Flatland/BA.2/2022,18,37,0,3,3,0.637900,0.310300,False,Omicron (BA.1-like),,S,T
Flatland/BA.3/2022,14,28,14,2,2,0.482800,0.241400,False,Omicron (BA.1-like),,S,T
Flatland/XE/2022,14,41,0,3,3,0.706900,0.241400,False,Omicron (BA.1-like),,S,T
40 changes: 20 additions & 20 deletions scorpio/tests/data/classify/expected.single_output_counts_classify.csv
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Original file line number Diff line number Diff line change
@@ -1,21 +1,21 @@
query,constellations,mrca_lineage,ref_count,alt_count,ambig_count,other_count,rule_count,support,conflict,constellation_name,call,note
Flatland/B.1.1.7/2021,48,8,0,3,1,0.135600,0.813600,False,Omicron (BA.1-like),
Flatland/B.1.351/2021,44,5,9,1,1,0.084700,0.745800,False,Omicron (BA.1-like),
Flatland/P.1/2021,49,7,0,3,1,0.118600,0.830500,False,Omicron (BA.1-like),
Flatland/P.1_again/2021,49,7,0,3,1,0.118600,0.830500,False,Omicron (BA.1-like),
Flatland/B.1.617.1/2021,48,4,2,5,1,0.067800,0.813600,False,Omicron (BA.1-like),
Flatland/B.1.617.2/2021,48,6,0,5,1,0.101700,0.813600,False,Omicron (BA.1-like),
Flatland/B.1.617.2_K417N/2021,46,6,0,7,1,0.101700,0.779700,False,Omicron (BA.1-like),
Flatland/AY.4/2021,47,7,0,5,1,0.118600,0.796600,False,Omicron (BA.1-like),
Flatland/AY.4.2/2021,46,7,1,5,1,0.118600,0.779700,False,Omicron (BA.1-like),
Flatland/B.1.427/2021,54,4,0,1,1,0.067800,0.915300,False,Omicron (BA.1-like),
Flatland/B.1.429/2021,55,3,0,1,1,0.050800,0.932200,False,Omicron (BA.1-like),
Flatland/B.1.526/2021,50,7,0,2,1,0.118600,0.847500,False,Omicron (BA.1-like),
Flatland/P.3/2021,47,7,0,5,1,0.118600,0.796600,False,Omicron (BA.1-like),
Flatland/B.1.525/2020,50,5,0,4,1,0.084700,0.847500,False,Omicron (BA.1-like),
Flatland/P.2/2021,52,4,0,3,1,0.067800,0.881400,False,Omicron (BA.1-like),
Flatland/C.37/2021,50,8,0,1,1,0.135600,0.847500,False,Omicron (BA.1-like),
Flatland/BA.1/2022,0,55,1,3,5,0.932200,0.000000,default,Omicron (BA.1-like),
Flatland/BA.2/2022,18,38,0,3,3,0.644100,0.305100,False,Omicron (BA.1-like),
Flatland/BA.3/2022,14,28,15,2,2,0.474600,0.237300,False,Omicron (BA.1-like),
Flatland/XE/2022,14,42,0,3,3,0.711900,0.237300,False,Omicron (BA.1-like),
Flatland/B.1.1.7/2021,47,8,0,3,1,0.137900,0.810300,False,Omicron (BA.1-like),
Flatland/B.1.351/2021,44,4,9,1,1,0.069000,0.758600,False,Omicron (BA.1-like),
Flatland/P.1/2021,49,7,0,2,1,0.120700,0.844800,False,Omicron (BA.1-like),
Flatland/P.1_again/2021,49,7,0,2,1,0.120700,0.844800,False,Omicron (BA.1-like),
Flatland/B.1.617.1/2021,47,4,2,5,1,0.069000,0.810300,False,Omicron (BA.1-like),
Flatland/B.1.617.2/2021,47,6,0,5,1,0.103400,0.810300,False,Omicron (BA.1-like),
Flatland/B.1.617.2_K417N/2021,46,5,0,7,1,0.086200,0.793100,False,Omicron (BA.1-like),
Flatland/AY.4/2021,46,7,0,5,1,0.120700,0.793100,False,Omicron (BA.1-like),
Flatland/AY.4.2/2021,45,7,1,5,1,0.120700,0.775900,False,Omicron (BA.1-like),
Flatland/B.1.427/2021,53,4,0,1,1,0.069000,0.913800,False,Omicron (BA.1-like),
Flatland/B.1.429/2021,54,3,0,1,1,0.051700,0.931000,False,Omicron (BA.1-like),
Flatland/B.1.526/2021,49,7,0,2,1,0.120700,0.844800,False,Omicron (BA.1-like),
Flatland/P.3/2021,46,7,0,5,1,0.120700,0.793100,False,Omicron (BA.1-like),
Flatland/B.1.525/2020,49,5,0,4,1,0.086200,0.844800,False,Omicron (BA.1-like),
Flatland/P.2/2021,51,4,0,3,1,0.069000,0.879300,False,Omicron (BA.1-like),
Flatland/C.37/2021,49,8,0,1,1,0.137900,0.844800,False,Omicron (BA.1-like),
Flatland/BA.1/2022,0,54,1,3,5,0.931000,0.000000,default,Omicron (BA.1-like),
Flatland/BA.2/2022,18,37,0,3,3,0.637900,0.310300,False,Omicron (BA.1-like),
Flatland/BA.3/2022,14,28,14,2,2,0.482800,0.241400,False,Omicron (BA.1-like),
Flatland/XE/2022,14,41,0,3,3,0.706900,0.241400,False,Omicron (BA.1-like),

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