From 4b81c9282576ead21c5ab2f66b943ec5aea69d4f Mon Sep 17 00:00:00 2001 From: Rachel Colquhoun Date: Mon, 21 Aug 2023 14:44:47 +0100 Subject: [PATCH] update based on latest constellations --- .../expected.multi_list_incompatible_long.csv | 2 +- ...ut_counts_classify.Omicron__BA.1-like_.csv | 40 +++++++++---------- ...ingle_mutations_output_counts_classify.csv | 40 +++++++++---------- ...expected.single_output_counts_classify.csv | 40 +++++++++---------- 4 files changed, 61 insertions(+), 61 deletions(-) diff --git a/scorpio/tests/data/classify/expected.multi_list_incompatible_long.csv b/scorpio/tests/data/classify/expected.multi_list_incompatible_long.csv index 27a5d67..671418e 100644 --- a/scorpio/tests/data/classify/expected.multi_list_incompatible_long.csv +++ b/scorpio/tests/data/classify/expected.multi_list_incompatible_long.csv @@ -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,,,,,,,,,,, diff --git a/scorpio/tests/data/classify/expected.multi_output_counts_classify.Omicron__BA.1-like_.csv b/scorpio/tests/data/classify/expected.multi_output_counts_classify.Omicron__BA.1-like_.csv index da96bb3..b856d78 100644 --- a/scorpio/tests/data/classify/expected.multi_output_counts_classify.Omicron__BA.1-like_.csv +++ b/scorpio/tests/data/classify/expected.multi_output_counts_classify.Omicron__BA.1-like_.csv @@ -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), diff --git a/scorpio/tests/data/classify/expected.single_mutations_output_counts_classify.csv b/scorpio/tests/data/classify/expected.single_mutations_output_counts_classify.csv index 4d7b966..7680112 100644 --- a/scorpio/tests/data/classify/expected.single_mutations_output_counts_classify.csv +++ b/scorpio/tests/data/classify/expected.single_mutations_output_counts_classify.csv @@ -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 diff --git a/scorpio/tests/data/classify/expected.single_output_counts_classify.csv b/scorpio/tests/data/classify/expected.single_output_counts_classify.csv index 8385d3c..300067a 100644 --- a/scorpio/tests/data/classify/expected.single_output_counts_classify.csv +++ b/scorpio/tests/data/classify/expected.single_output_counts_classify.csv @@ -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),