Add H10 and new H7 ref (#645)

* Add H10 and new H7 ref * Fix typos, add processed files
vector-engineering · May 11, 2024 · ecdd12b · ecdd12b
1 parent 8ae0710
commit ecdd12b
Show file tree

Hide file tree

Showing 63 changed files with 3,938 additions and 151 deletions.
diff --git a/config/config_flu_genbank.yaml b/config/config_flu_genbank.yaml
@@ -92,6 +92,7 @@ report_group_references:
   H5NX: A-Goose-Guangdong-1-96
   H7NX: A-Shanghai-02-2013
   H9NX: A-Hong-Kong-1073-99
+  H10NX: A-Jiangsu-428-2021
 
 # Surveillance plot options
 # see: workflow_main/scripts/surveillance.py
@@ -110,6 +111,7 @@ surv_group_references:
   H5NX: A-Goose-Guangdong-1-96
   H7NX: A-Shanghai-02-2013
   H9NX: A-Hong-Kong-1073-99
+  H10NX: A-Jiangsu-428-2021
 
 # ---------------
 #    DATABASE
@@ -151,6 +153,7 @@ default_references:
   H5NX: A-Goose-Guangdong-1-96
   H7NX: A-Shanghai-02-2013
   H9NX: A-Hong-Kong-1073-99
+  H10NX: A-Jiangsu-428-2021
 
 # Home page
 show_home_banner: false

diff --git a/config/config_flu_gisaid.yaml b/config/config_flu_gisaid.yaml
@@ -120,6 +120,7 @@ report_group_references:
   H5NX: A-Viet-Nam-1203-2004
   H7NX: A-Shanghai-02-2013
   H9NX: A-Hong-Kong-1073-99
+  H10NX: A-Jiangsu-428-2021
 
 # Surveillance plot options
 # see: workflow_main/scripts/surveillance.py
@@ -138,6 +139,7 @@ surv_group_references:
   H5NX: A-Viet-Nam-1203-2004
   H7NX: A-Shanghai-02-2013
   H9NX: A-Hong-Kong-1073-99
+  H10NX: A-Jiangsu-428-2021
 
 # ---------------
 #    DATABASE
@@ -180,6 +182,7 @@ default_references:
   H5NX: A-Viet-Nam-1203-2004
   H7NX: A-Shanghai-02-2013
   H9NX: A-Hong-Kong-1073-99
+  H10NX: A-Jiangsu-428-2021
 
 # Home page
 show_home_banner: false

diff --git a/config/config_flu_gisaid_dev.yaml b/config/config_flu_gisaid_dev.yaml
@@ -125,6 +125,7 @@ report_group_references:
   H5NX: A-Goose-Guangdong-1-96
   H7NX: A-Shanghai-02-2013
   H9NX: A-Hong-Kong-1073-99
+  H10NX: A-Jiangsu-428-2021
 
 # Surveillance plot options
 # see: workflow_main/scripts/surveillance.py
@@ -143,6 +144,7 @@ surv_group_references:
   H5NX: A-Goose-Guangdong-1-96
   H7NX: A-Shanghai-02-2013
   H9NX: A-Hong-Kong-1073-99
+  H10NX: A-Jiangsu-428-2021
 
 # ---------------
 #    DATABASE
@@ -185,6 +187,7 @@ default_references:
   H5NX: A-Goose-Guangdong-1-96
   H7NX: A-Shanghai-02-2013
   H9NX: A-Hong-Kong-1073-99
+  H10NX: A-Jiangsu-428-2021
 
 # Home page
 show_home_banner: false

diff --git a/static_data/flu/alignments/H10N8_1.dna b/static_data/flu/alignments/H10N8_1.dna
diff --git a/static_data/flu/alignments/H10N8_2.dna b/static_data/flu/alignments/H10N8_2.dna
diff --git a/static_data/flu/alignments/H10N8_3.dna b/static_data/flu/alignments/H10N8_3.dna
diff --git a/static_data/flu/alignments/H10N8_4.dna b/static_data/flu/alignments/H10N8_4.dna
diff --git a/static_data/flu/alignments/H10N8_5.dna b/static_data/flu/alignments/H10N8_5.dna
diff --git a/static_data/flu/alignments/H10N8_6.dna b/static_data/flu/alignments/H10N8_6.dna
diff --git a/static_data/flu/alignments/H10N8_7.dna b/static_data/flu/alignments/H10N8_7.dna
diff --git a/static_data/flu/alignments/H10N8_8.dna b/static_data/flu/alignments/H10N8_8.dna
diff --git a/static_data/flu/alignments/H7N2_1_NC_026422.dna b/static_data/flu/alignments/H7N2_1_NC_026422.dna
diff --git a/static_data/flu/alignments/H7N2_2_NC_026423.dna b/static_data/flu/alignments/H7N2_2_NC_026423.dna
diff --git a/static_data/flu/alignments/H7N2_3_NC_026424.dna b/static_data/flu/alignments/H7N2_3_NC_026424.dna
diff --git a/static_data/flu/alignments/H7N2_4_NC_026425.dna b/static_data/flu/alignments/H7N2_4_NC_026425.dna
diff --git a/static_data/flu/alignments/H7N2_5_NC_026426.dna b/static_data/flu/alignments/H7N2_5_NC_026426.dna
diff --git a/static_data/flu/alignments/H7N2_6_NC_026429.dna b/static_data/flu/alignments/H7N2_6_NC_026429.dna
diff --git a/static_data/flu/alignments/H7N2_7_NC_026427.dna b/static_data/flu/alignments/H7N2_7_NC_026427.dna
diff --git a/static_data/flu/alignments/H7N2_8_NC_026428.dna b/static_data/flu/alignments/H7N2_8_NC_026428.dna
diff --git a/static_data/flu/alignments/HA_all.praln b/static_data/flu/alignments/HA_all.praln
diff --git a/static_data/flu/genes.csv b/static_data/flu/genes.csv
@@ -138,6 +138,16 @@ H7NX,A-Shanghai-02-2013,M1,7,1..759,1,0,[],
 H7NX,A-Shanghai-02-2013,M2,7,1..26;715..982,1,0,[],
 H7NX,A-Shanghai-02-2013,NEP,8,1..30;503..838,1,0,[],
 H7NX,A-Shanghai-02-2013,NS1,8,1..654,1,0,[],
+H7NX,A-Anhui-1-2013,PB2,1,1..2280,1,0,[],
+H7NX,A-Anhui-1-2013,PB1,2,1..2274,1,0,[],
+H7NX,A-Anhui-1-2013,PA,3,1..2151,1,0,[],
+H7NX,A-Anhui-1-2013,HA,4,1..1683,1,18,"[{""name"": ""signal peptide"", ""ranges"": [[1, 18]]}, {""name"": ""HA1"", ""ranges"": [[19, 339]]}, {""name"": ""HA2"", ""ranges"": [[340, 560]]}]",
+H7NX,A-Anhui-1-2013,NP,5,1..1497,1,0,[],
+H7NX,A-Anhui-1-2013,NA,6,1..1398,1,0,[],
+H7NX,A-Anhui-1-2013,M1,7,1..759,1,0,[],
+H7NX,A-Anhui-1-2013,M2,7,1..26;715..982,1,0,[],
+H7NX,A-Anhui-1-2013,NEP,8,1..30;503..838,1,0,[],
+H7NX,A-Anhui-1-2013,NS1,8,1..654,1,0,[],
 H9NX,A-Hong-Kong-1073-99,PB2,1,28..2307,1,0,[],
 H9NX,A-Hong-Kong-1073-99,PB1,2,24..2300,1,0,[],
 H9NX,A-Hong-Kong-1073-99,PA,3,21..2171,1,0,[],
@@ -148,6 +158,26 @@ H9NX,A-Hong-Kong-1073-99,M1,7,33..791,1,0,[],
 H9NX,A-Hong-Kong-1073-99,M2,7,33..59;748..1014,1,0,[],
 H9NX,A-Hong-Kong-1073-99,NEP,8,27..56;529..864,1,0,[],
 H9NX,A-Hong-Kong-1073-99,NS1,8,27..719,1,0,[],
+H10NX,A-Jiangsu-428-2021,PB2,1,28..2307,1,0,[],
+H10NX,A-Jiangsu-428-2021,PB1,2,25..2298,1,0,[],
+H10NX,A-Jiangsu-428-2021,PA,3,25..2175,1,0,[],
+H10NX,A-Jiangsu-428-2021,HA,4,20..1705,1,16,"[{""name"": ""signal peptide"", ""ranges"": [[1, 16]]}, {""name"": ""HA1"", ""ranges"": [[17, 340]]}, {""name"": ""HA2"", ""ranges"": [[341, 561]]}]",
+H10NX,A-Jiangsu-428-2021,NP,5,46..1542,1,0,[],
+H10NX,A-Jiangsu-428-2021,NA,6,19..1428,1,0,[],
+H10NX,A-Jiangsu-428-2021,M1,7,26..784,1,0,[],
+H10NX,A-Jiangsu-428-2021,M2,7,26..51;740..1007,1,0,[],
+H10NX,A-Jiangsu-428-2021,NS1,8,27..680,1,0,[],
+H10NX,A-Jiangsu-428-2021,NEP,8,27..56;529..864,1,0,[],
+H10NX,A-Jiangxi-Donghu-346-2013,PB2,1,1..2280,1,0,[],
+H10NX,A-Jiangxi-Donghu-346-2013,PB1,2,1..2274,1,0,[],
+H10NX,A-Jiangxi-Donghu-346-2013,PA,3,1..2151,1,0,[],
+H10NX,A-Jiangxi-Donghu-346-2013,HA,4,1..1686,1,16,"[{""name"": ""signal peptide"", ""ranges"": [[1, 16]]}, {""name"": ""HA1"", ""ranges"": [[17, 340]]}, {""name"": ""HA2"", ""ranges"": [[341, 561]]}]",
+H10NX,A-Jiangxi-Donghu-346-2013,NP,5,1..1497,1,0,[],
+H10NX,A-Jiangxi-Donghu-346-2013,NA,6,1..1413,1,0,[],
+H10NX,A-Jiangxi-Donghu-346-2013,M1,7,1..759,1,0,[],
+H10NX,A-Jiangxi-Donghu-346-2013,M2,7,1..26;715..982,1,0,[],
+H10NX,A-Jiangxi-Donghu-346-2013,NS1,8,1..654,1,0,[],
+H10NX,A-Jiangxi-Donghu-346-2013,NEP,8,1..30;503..838,1,0,[],
 B-yam,B-Massachusetts-02-2012,HA,4,1..1755,1,15,"[{""name"": ""signal peptide"", ""ranges"": [[1, 15]]}, {""name"": ""HA1"", ""ranges"": [[16, 361]]}, {""name"": ""HA2"", ""ranges"": [[362, 584]]}]",
 B-yam,B-Massachusetts-02-2012,NA,6,1..1401,1,0,[],
 B-yam,B-Massachusetts-02-2012,NB,6,3..296,1,0,[],