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update hivdb#956, fix Hu23
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KaimingTao committed Sep 18, 2023
1 parent d3e346b commit f284af0
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Showing 11 changed files with 531 additions and 470 deletions.
3 changes: 2 additions & 1 deletion tables/articles.csv
Original file line number Diff line number Diff line change
Expand Up @@ -679,7 +679,7 @@ Oliveira22,10.1101/2022.07.31.502215,NULL,"Oliveira, VMD",2022,2022-11-08,NULL
FDA21d,NULL,https://www.fda.gov/media/155050/download,FDA,2021,2022-11-08,2022-11-20
Moghadasi22,10.1101/2022.08.07.503099,NULL,"Moghadasi, SA",2022,2022-11-09,NULL
Miller23,10.1056/NEJMc2214314,NULL,"Miller, J",2023,2022-11-09,2023-04-04
Tan22,10.1021/acs.accounts.2c00735,NULL,"Tan, B",2022,2022-11-09,2023-03-28
Tan23,10.1021/acs.accounts.2c00735,NULL,"Tan, B",2022,2022-11-09,2023-03-28
Kurhade23,10.1038/s41591-022-02162-x,NULL,"Kurhade, C",2023,2022-11-09,2023-04-04
Atari22,10.2807/1560-7917.ES.2022.27.44.2200785,NULL,"Atari, N",2022,2022-11-09,NULL
Ou22,10.1101/2022.08.06.503039,NULL,"Ou, J",2022,2022-11-09,NULL
Expand Down Expand Up @@ -791,3 +791,4 @@ Lin23,10.1038/s42003-023-05071-y,NULL,"Lin, M",2023,2023-08-16,NULL
Takashita23,10.1016/j.antiviral.2023.105671,NULL,"Takashita, E",2023,2023-08-16,NULL
Flynn23,10.1021/acsinfecdis.3c00125,NULL,"Flynn, JM",2023,2023-08-16,NULL
Yang23,10.1101/2023.09.01.555815,NULL,"Yang, S",2023,2023-09-11,NULL
Hu23,10.1021/acscentsci.3c00538,NULL,"Hu, Y",2023,2023-09-18,NULL
2 changes: 1 addition & 1 deletion tables/articles_preprint_doi.csv
Original file line number Diff line number Diff line change
Expand Up @@ -232,7 +232,7 @@ Rothenberger22,10.1101/2021.02.03.429164
Muik22,10.1101/2021.12.22.21268103
Zou23,10.1101/2022.11.17.516898
Wang22l,10.1101/2022.11.23.517532
Tan22,10.1101/2022.06.28.497978
Hu23,10.1101/2022.06.28.497978
Zhou22c,10.1101/2022.06.06.494921
Maponga22,10.2139/ssrn.4014499
Noske23,10.1101/2022.08.31.506107
Expand Down
Original file line number Diff line number Diff line change
@@ -1,12 +1,15 @@
iso_name,gene,position,amino_acid,count,total
3CLpro:M49L,_3CLpro,49,L,NULL,NULL
3CLpro:M49V,_3CLpro,49,V,NULL,NULL
3CLpro:M49del,_3CLpro,49,del,NULL,NULL
3CLpro:T135del,_3CLpro,135,del,NULL,NULL
3CLpro:N142I,_3CLpro,142,I,NULL,NULL
3CLpro:N142H,_3CLpro,142,H,NULL,NULL
3CLpro:N142M,_3CLpro,142,M,NULL,NULL
3CLpro:N142K,_3CLpro,142,K,NULL,NULL
3CLpro:N142T,_3CLpro,142,T,NULL,NULL
3CLpro:N142Y,_3CLpro,142,Y,NULL,NULL
3CLpro:N142del,_3CLpro,142,del,NULL,NULL
3CLpro:S144L,_3CLpro,144,L,NULL,NULL
3CLpro:S144T,_3CLpro,144,T,NULL,NULL
3CLpro:S144M,_3CLpro,144,M,NULL,NULL
Expand All @@ -18,10 +21,14 @@
3CLpro:S144H,_3CLpro,144,H,NULL,NULL
3CLpro:S144Q,_3CLpro,144,Q,NULL,NULL
3CLpro:S144R,_3CLpro,144,R,NULL,NULL
3CLpro:L50F+S144M,_3CLpro,50,F,NULL,NULL
3CLpro:L50F+S144M,_3CLpro,144,M,NULL,NULL
3CLpro:S144G,_3CLpro,144,G,NULL,NULL
3CLpro:S144Y,_3CLpro,144,Y,NULL,NULL
3CLpro:S144K,_3CLpro,144,K,NULL,NULL
3CLpro:S144D,_3CLpro,144,D,NULL,NULL
3CLpro:S144del,_3CLpro,144,del,NULL,NULL
3CLpro:S164del,_3CLpro,164,del,NULL,NULL
3CLpro:M165Y,_3CLpro,165,Y,NULL,NULL
3CLpro:M165L,_3CLpro,165,L,NULL,NULL
3CLpro:M165V,_3CLpro,165,V,NULL,NULL
Expand All @@ -36,13 +43,17 @@
3CLpro:M165P,_3CLpro,165,P,NULL,NULL
3CLpro:M165C,_3CLpro,165,C,NULL,NULL
3CLpro:M165D,_3CLpro,165,D,NULL,NULL
3CLpro:M165del,_3CLpro,165,del,NULL,NULL
3CLpro:E166Q,_3CLpro,166,Q,NULL,NULL
3CLpro:E166H,_3CLpro,166,H,NULL,NULL
3CLpro:E166G,_3CLpro,166,G,NULL,NULL
3CLpro:E166K,_3CLpro,166,K,NULL,NULL
3CLpro:E166L,_3CLpro,166,L,NULL,NULL
3CLpro:E166Y,_3CLpro,166,Y,NULL,NULL
3CLpro:E166I,_3CLpro,166,I,NULL,NULL
3CLpro:E166V,_3CLpro,166,V,NULL,NULL
3CLpro:E166A,_3CLpro,166,A,NULL,NULL
3CLpro:E166del,_3CLpro,166,del,NULL,NULL
3CLpro:H172T,_3CLpro,172,T,NULL,NULL
3CLpro:H172E,_3CLpro,172,E,NULL,NULL
3CLpro:H172Q,_3CLpro,172,Q,NULL,NULL
Expand All @@ -59,12 +70,14 @@
3CLpro:H172R,_3CLpro,172,R,NULL,NULL
3CLpro:H172G,_3CLpro,172,G,NULL,NULL
3CLpro:H172C,_3CLpro,172,C,NULL,NULL
3CLpro:H172del,_3CLpro,172,del,NULL,NULL
3CLpro:Q189F,_3CLpro,189,F,NULL,NULL
3CLpro:Q189R,_3CLpro,189,R,NULL,NULL
3CLpro:Q189P,_3CLpro,189,P,NULL,NULL
3CLpro:Q189H,_3CLpro,189,H,NULL,NULL
3CLpro:Q189L,_3CLpro,189,L,NULL,NULL
3CLpro:Q189S,_3CLpro,189,S,NULL,NULL
3CLpro:Q189del,_3CLpro,189,del,NULL,NULL
3CLpro:Q192K,_3CLpro,192,K,NULL,NULL
3CLpro:Q192S,_3CLpro,192,S,NULL,NULL
3CLpro:Q192L,_3CLpro,192,L,NULL,NULL
Expand All @@ -81,5 +94,6 @@
3CLpro:Q192C,_3CLpro,192,C,NULL,NULL
3CLpro:Q192D,_3CLpro,192,D,NULL,NULL
3CLpro:Q192F,_3CLpro,192,F,NULL,NULL
3CLpro:Q192del,_3CLpro,192,del,NULL,NULL
3CLpro:Q189E+H172Y,_3CLpro,189,E,NULL,NULL
3CLpro:Q189E+H172Y,_3CLpro,172,Y,NULL,NULL
111 changes: 111 additions & 0 deletions tables/ref_isolate_pairs/hu23-pair.csv
Original file line number Diff line number Diff line change
@@ -0,0 +1,111 @@
ref_name,control_iso_name,iso_name
Hu23,Wuhan-Hu-1,3CLpro:M49I
Hu23,Wuhan-Hu-1,3CLpro:M49T
Hu23,Wuhan-Hu-1,3CLpro:M49L
Hu23,Wuhan-Hu-1,3CLpro:M49V
Hu23,Wuhan-Hu-1,3CLpro:M49del
Hu23,Wuhan-Hu-1,3CLpro:T135I
Hu23,Wuhan-Hu-1,3CLpro:T135del
Hu23,Wuhan-Hu-1,3CLpro:N142S
Hu23,Wuhan-Hu-1,3CLpro:N142D
Hu23,Wuhan-Hu-1,3CLpro:N142L
Hu23,Wuhan-Hu-1,3CLpro:N142I
Hu23,Wuhan-Hu-1,3CLpro:N142H
Hu23,Wuhan-Hu-1,3CLpro:N142M
Hu23,Wuhan-Hu-1,3CLpro:N142K
Hu23,Wuhan-Hu-1,3CLpro:N142T
Hu23,Wuhan-Hu-1,3CLpro:N142Y
Hu23,Wuhan-Hu-1,3CLpro:N142del
Hu23,Wuhan-Hu-1,3CLpro:S144L
Hu23,Wuhan-Hu-1,3CLpro:S144T
Hu23,Wuhan-Hu-1,3CLpro:S144M
Hu23,Wuhan-Hu-1,3CLpro:L50F+S144M
Hu23,Wuhan-Hu-1,3CLpro:S144F
Hu23,Wuhan-Hu-1,3CLpro:S144P
Hu23,Wuhan-Hu-1,3CLpro:S144A
Hu23,Wuhan-Hu-1,3CLpro:S144W
Hu23,Wuhan-Hu-1,3CLpro:S144E
Hu23,Wuhan-Hu-1,3CLpro:S144V
Hu23,Wuhan-Hu-1,3CLpro:S144H
Hu23,Wuhan-Hu-1,3CLpro:S144Q
Hu23,Wuhan-Hu-1,3CLpro:S144R
Hu23,Wuhan-Hu-1,3CLpro:S144G
Hu23,Wuhan-Hu-1,3CLpro:S144Y
Hu23,Wuhan-Hu-1,3CLpro:S144K
Hu23,Wuhan-Hu-1,3CLpro:S144D
Hu23,Wuhan-Hu-1,3CLpro:S144del
Hu23,Wuhan-Hu-1,3CLpro:H164N
Hu23,Wuhan-Hu-1,3CLpro:H164del
Hu23,Wuhan-Hu-1,3CLpro:M165Y
Hu23,Wuhan-Hu-1,3CLpro:M165L
Hu23,Wuhan-Hu-1,3CLpro:M165I
Hu23,Wuhan-Hu-1,3CLpro:M165V
Hu23,Wuhan-Hu-1,3CLpro:M165W
Hu23,Wuhan-Hu-1,3CLpro:M165K
Hu23,Wuhan-Hu-1,3CLpro:M165T
Hu23,Wuhan-Hu-1,3CLpro:M165R
Hu23,Wuhan-Hu-1,3CLpro:M165A
Hu23,Wuhan-Hu-1,3CLpro:M165G
Hu23,Wuhan-Hu-1,3CLpro:M165F
Hu23,Wuhan-Hu-1,3CLpro:M165H
Hu23,Wuhan-Hu-1,3CLpro:M165P
Hu23,Wuhan-Hu-1,3CLpro:M165C
Hu23,Wuhan-Hu-1,3CLpro:M165D
Hu23,Wuhan-Hu-1,3CLpro:M165del
Hu23,Wuhan-Hu-1,3CLpro:E166Q
Hu23,Wuhan-Hu-1,3CLpro:E166H
Hu23,Wuhan-Hu-1,3CLpro:E166G
Hu23,Wuhan-Hu-1,3CLpro:E166K
Hu23,Wuhan-Hu-1,3CLpro:H166V
Hu23,Wuhan-Hu-1,3CLpro:H166A
Hu23,Wuhan-Hu-1,3CLpro:E166L
Hu23,Wuhan-Hu-1,3CLpro:E166Y
Hu23,Wuhan-Hu-1,3CLpro:E166I
Hu23,Wuhan-Hu-1,3CLpro:E166del
Hu23,Wuhan-Hu-1,3CLpro:H172T
Hu23,Wuhan-Hu-1,3CLpro:H172Y
Hu23,Wuhan-Hu-1,3CLpro:H172E
Hu23,Wuhan-Hu-1,3CLpro:H172Q
Hu23,Wuhan-Hu-1,3CLpro:H172D
Hu23,Wuhan-Hu-1,3CLpro:H172L
Hu23,Wuhan-Hu-1,3CLpro:H172M
Hu23,Wuhan-Hu-1,3CLpro:H172A
Hu23,Wuhan-Hu-1,3CLpro:H172F
Hu23,Wuhan-Hu-1,3CLpro:H172I
Hu23,Wuhan-Hu-1,3CLpro:H172V
Hu23,Wuhan-Hu-1,3CLpro:H172N
Hu23,Wuhan-Hu-1,3CLpro:H172S
Hu23,Wuhan-Hu-1,3CLpro:H172K
Hu23,Wuhan-Hu-1,3CLpro:H172R
Hu23,Wuhan-Hu-1,3CLpro:H172G
Hu23,Wuhan-Hu-1,3CLpro:H172C
Hu23,Wuhan-Hu-1,3CLpro:H172del
Hu23,Wuhan-Hu-1,3CLpro:Q189K
Hu23,Wuhan-Hu-1,3CLpro:Q189F
Hu23,Wuhan-Hu-1,3CLpro:Q189R
Hu23,Wuhan-Hu-1,3CLpro:Q189H
Hu23,Wuhan-Hu-1,3CLpro:Q189L
Hu23,Wuhan-Hu-1,3CLpro:Q189P
Hu23,Wuhan-Hu-1,3CLpro:Q189S
Hu23,Wuhan-Hu-1,3CLpro:Q189E
Hu23,Wuhan-Hu-1,3CLpro:Q189del
Hu23,Wuhan-Hu-1,3CLpro:Q192T
Hu23,Wuhan-Hu-1,3CLpro:Q192K
Hu23,Wuhan-Hu-1,3CLpro:Q192S
Hu23,Wuhan-Hu-1,3CLpro:Q192L
Hu23,Wuhan-Hu-1,3CLpro:Q192R
Hu23,Wuhan-Hu-1,3CLpro:Q192N
Hu23,Wuhan-Hu-1,3CLpro:Q192A
Hu23,Wuhan-Hu-1,3CLpro:Q192I
Hu23,Wuhan-Hu-1,3CLpro:Q192P
Hu23,Wuhan-Hu-1,3CLpro:Q192G
Hu23,Wuhan-Hu-1,3CLpro:Q192H
Hu23,Wuhan-Hu-1,3CLpro:Q192Y
Hu23,Wuhan-Hu-1,3CLpro:Q192V
Hu23,Wuhan-Hu-1,3CLpro:Q192W
Hu23,Wuhan-Hu-1,3CLpro:Q192E
Hu23,Wuhan-Hu-1,3CLpro:Q192C
Hu23,Wuhan-Hu-1,3CLpro:Q192D
Hu23,Wuhan-Hu-1,3CLpro:Q192F
Hu23,Wuhan-Hu-1,3CLpro:Q192del
Hu23,Wuhan-Hu-1,3CLpro:Q189E+H172Y
98 changes: 0 additions & 98 deletions tables/ref_isolate_pairs/tan22-pair.csv

This file was deleted.

5 changes: 5 additions & 0 deletions tables/rx_compounds/hu23-drug.csv
Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
ref_name,rx_name,drug_name
Hu23,GC376,GC376
Hu23,PF-00835231,PF-00835231
Hu23,Nirmatrelvir pre-print,Nirmatrelvir
Hu23,Nirmatrelvir,Nirmatrelvir
5 changes: 0 additions & 5 deletions tables/rx_compounds/tan22-drug.csv

This file was deleted.

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