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Add 9 autorefs to lineage_notes.txt #2167

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merged 4 commits into from
Aug 15, 2023
Merged

Add 9 autorefs to lineage_notes.txt #2167

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371da2d
add 9 autorefs to lineage_notes.txt
xz-keg Aug 6, 2023
4bd8a9f
Merge branch 'cov-lineages:master' into master
xz-keg Aug 7, 2023
3177d1b
Merge branch 'master' into master
xz-keg Aug 11, 2023
026c92d
Merge branch 'master' into master
AngieHinrichs Aug 15, 2023
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84 changes: 21 additions & 63 deletions automated-issue-ref.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
"execution_count": 41,
"execution_count": 1,
"id": "f64573a2",
"metadata": {},
"outputs": [],
Expand All @@ -16,7 +16,7 @@
"start_milestone=1\n",
"start_sub_milestone=1\n",
"end_milestone=801\n",
"end_sub_milestone=51\n",
"end_sub_milestone=59\n",
"def read_milestone(num,di='cov-lineages/pango-designation',output_format='sep'):\n",
" # or sars-cov-2 proj if it starts to add milestones\n",
" url=\"https://github.com/\"+di+\"/milestone/\"+str(num)\n",
Expand Down Expand Up @@ -47,7 +47,7 @@
},
{
"cell_type": "code",
"execution_count": 16,
"execution_count": 2,
"id": "769f2d32",
"metadata": {
"scrolled": false
Expand All @@ -57,13 +57,10 @@
"name": "stdout",
"output_type": "stream",
"text": [
"Reading Milestone 40\n",
"Reading Milestone 440\n",
"Reading Milestone 610\n",
"801 HTTP Error 404: Not Found\n",
"10 HTTP Error 404: Not Found\n",
"Reading Milestone in sars-cov-2-variants 30\n",
"51 HTTP Error 404: Not Found\n"
"59 HTTP Error 404: Not Found\n",
"Reading Milestone in sars-cov-2-variants 60\n"
]
}
],
Expand Down Expand Up @@ -165,7 +162,7 @@
},
{
"cell_type": "code",
"execution_count": 39,
"execution_count": 3,
"id": "88a367db",
"metadata": {},
"outputs": [],
Expand Down Expand Up @@ -212,7 +209,7 @@
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": 4,
"id": "f5b15585",
"metadata": {},
"outputs": [],
Expand All @@ -235,63 +232,24 @@
},
{
"cell_type": "code",
"execution_count": 42,
"execution_count": 5,
"id": "a56544a8",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"['FK.1.1.1', 'sars-cov-2-variants/lineage-proposals#368']\n",
"['FK.1.4.1', 'sars-cov-2-variants/lineage-proposals#88']\n",
"['HM.1', 'sars-cov-2-variants/lineage-proposals#59']\n",
"39\n",
"FT.3+FT.3.1\n",
"['FT.3', 'sars-cov-2-variants/lineage-proposals#266']\n",
"39\n",
"FT.3+FT.3.1\n",
"['FT.3.1', 'sars-cov-2-variants/lineage-proposals#266']\n",
"['FT.3.1.1', '#2140']\n",
"['HR.1', 'sars-cov-2-variants/lineage-proposals#323']\n",
"['HP.1', 'sars-cov-2-variants/lineage-proposals#277']\n",
"['HP.1.1', 'sars-cov-2-variants/lineage-proposals#277']\n",
"['HZ.1', 'sars-cov-2-variants/lineage-proposals#514']\n",
"HQ.1 list index out of range\n",
"31\n",
"XBB.1.5.93+HD.1++HD.1.1\n",
"['XBB.1.5.93', 'sars-cov-2-variants/lineage-proposals#363']\n",
"31\n",
"XBB.1.5.93+HD.1++HD.1.1\n",
"['HD.1.1', 'sars-cov-2-variants/lineage-proposals#363']\n",
"['HN.1', 'sars-cov-2-variants/lineage-proposals#408']\n",
"['FL.21.1', '#2143']\n",
"['FL.21.2', 'sars-cov-2-variants/lineage-proposals#187']\n",
"['FL.29', 'sars-cov-2-variants/lineage-proposals#119']\n",
"['HK.1', 'sars-cov-2-variants/lineage-proposals#359']\n",
"['HK.2', 'sars-cov-2-variants/lineage-proposals#432']\n",
"['HK.3', 'sars-cov-2-variants/lineage-proposals#414']\n",
"['EG.5.1.3', 'sars-cov-2-variants/lineage-proposals#222']\n",
"['EG.5.1.4', 'sars-cov-2-variants/lineage-proposals#428']\n",
"['EG.5.1.6', 'sars-cov-2-variants/lineage-proposals#394']\n",
"['EG.5.2.1', 'sars-cov-2-variants/lineage-proposals#189']\n",
"['EG.5.2.3', 'sars-cov-2-variants/lineage-proposals#353']\n",
"['EG.9', 'sars-cov-2-variants/lineage-proposals#280']\n",
"['EG.9.1', 'sars-cov-2-variants/lineage-proposals#57']\n",
"38\n",
"EG.10++EG.10.1\n",
"['EG.10', 'sars-cov-2-variants/lineage-proposals#346']\n",
"38\n",
"EG.10++EG.10.1\n",
"['EG.10.1', 'sars-cov-2-variants/lineage-proposals#346']\n",
"['GY.4', 'sars-cov-2-variants/lineage-proposals#345']\n",
"['XBB.1.16.17', 'sars-cov-2-variants/lineage-proposals#354']\n",
"['XBB.1.16.18', 'sars-cov-2-variants/lineage-proposals#276']\n",
"['GA.4', 'sars-cov-2-variants/lineage-proposals#265']\n",
"['GW.5', 'sars-cov-2-variants/lineage-proposals#61']\n",
"['XBB.1.19.2', 'sars-cov-2-variants/lineage-proposals#233']\n",
"['FY.4.1.1', 'sars-cov-2-variants/lineage-proposals#302']\n",
"['FY.7', 'sars-cov-2-variants/lineage-proposals#257']\n",
"['HU.2', 'sars-cov-2-variants/lineage-proposals#364']\n",
"['XBB.1.31.1', 'sars-cov-2-variants/lineage-proposals#141']\n",
"['HL.1', 'sars-cov-2-variants/lineage-proposals#352']\n"
"['HY.1', 'sars-cov-2-variants/lineage-proposals#453']\n",
"['EG.5.1.2', 'sars-cov-2-variants/lineage-proposals#301']\n",
"['FP.2.1.1', 'sars-cov-2-variants/lineage-proposals#329']\n",
"['GJ.1.2.1', 'sars-cov-2-variants/lineage-proposals#446']\n",
"['HW.1', 'sars-cov-2-variants/lineage-proposals#71']\n",
"['HW.1.1', 'sars-cov-2-variants/lineage-proposals#452']\n"
]
}
],
Expand Down Expand Up @@ -358,16 +316,16 @@
},
{
"cell_type": "code",
"execution_count": 43,
"execution_count": 6,
"id": "1c9369e1",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Add 2 references from cov-lineages/pango-designation.\n",
"Add 34 references from sars-cov-2-variants/lineage-proposals.\n"
"Add 0 references from cov-lineages/pango-designation.\n",
"Add 9 references from sars-cov-2-variants/lineage-proposals.\n"
]
}
],
Expand Down Expand Up @@ -405,7 +363,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 2,
"id": "7756372f",
"metadata": {},
"outputs": [],
Expand Down
10 changes: 10 additions & 0 deletions autoref/milestone_sub.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -52,3 +52,13 @@
29 nothing
30 nothing
40 nothing
51 XBB.1.16.14
51 FP.2.1.1
52 EG.5.1.2
53 HP.1
53 HP.1.1
54 HW.1.1
55 HY.1
56 GJ.1.2.1
57 HZ.1
58 HW.1
45 changes: 9 additions & 36 deletions autoref/missing_refs.txt
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Original file line number Diff line number Diff line change
@@ -1,36 +1,9 @@
FK.1.1.1 sars-cov-2-variants/lineage-proposals#368
FK.1.4.1 sars-cov-2-variants/lineage-proposals#88
HM.1 sars-cov-2-variants/lineage-proposals#59
FT.3 sars-cov-2-variants/lineage-proposals#266
FT.3.1 sars-cov-2-variants/lineage-proposals#266
FT.3.1.1 #2140
HR.1 sars-cov-2-variants/lineage-proposals#323
XBB.1.5.93 sars-cov-2-variants/lineage-proposals#363
HD.1.1 sars-cov-2-variants/lineage-proposals#363
HN.1 sars-cov-2-variants/lineage-proposals#408
FL.21.1 #2143
FL.21.2 sars-cov-2-variants/lineage-proposals#187
FL.29 sars-cov-2-variants/lineage-proposals#119
HK.1 sars-cov-2-variants/lineage-proposals#359
HK.2 sars-cov-2-variants/lineage-proposals#432
HK.3 sars-cov-2-variants/lineage-proposals#414
EG.5.1.3 sars-cov-2-variants/lineage-proposals#222
EG.5.1.4 sars-cov-2-variants/lineage-proposals#428
EG.5.1.6 sars-cov-2-variants/lineage-proposals#394
EG.5.2.1 sars-cov-2-variants/lineage-proposals#189
EG.5.2.3 sars-cov-2-variants/lineage-proposals#353
EG.9 sars-cov-2-variants/lineage-proposals#280
EG.9.1 sars-cov-2-variants/lineage-proposals#57
EG.10 sars-cov-2-variants/lineage-proposals#346
EG.10.1 sars-cov-2-variants/lineage-proposals#346
GY.4 sars-cov-2-variants/lineage-proposals#345
XBB.1.16.17 sars-cov-2-variants/lineage-proposals#354
XBB.1.16.18 sars-cov-2-variants/lineage-proposals#276
GA.4 sars-cov-2-variants/lineage-proposals#265
GW.5 sars-cov-2-variants/lineage-proposals#61
XBB.1.19.2 sars-cov-2-variants/lineage-proposals#233
FY.4.1.1 sars-cov-2-variants/lineage-proposals#302
FY.7 sars-cov-2-variants/lineage-proposals#257
HU.2 sars-cov-2-variants/lineage-proposals#364
XBB.1.31.1 sars-cov-2-variants/lineage-proposals#141
HL.1 sars-cov-2-variants/lineage-proposals#352
HP.1 sars-cov-2-variants/lineage-proposals#277
HP.1.1 sars-cov-2-variants/lineage-proposals#277
HZ.1 sars-cov-2-variants/lineage-proposals#514
HY.1 sars-cov-2-variants/lineage-proposals#453
EG.5.1.2 sars-cov-2-variants/lineage-proposals#301
FP.2.1.1 sars-cov-2-variants/lineage-proposals#329
GJ.1.2.1 sars-cov-2-variants/lineage-proposals#446
HW.1 sars-cov-2-variants/lineage-proposals#71
HW.1.1 sars-cov-2-variants/lineage-proposals#452
18 changes: 9 additions & 9 deletions lineage_notes.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -2769,8 +2769,8 @@ JB.1 Alias of XBB.1.5.53.1, S:N148T, South Africa
JB.2 Alias of XBB.1.5.53.2, S:K478R, South Africa/USA
XBB.1.5.54 C14358T,C20016T,C29311T, Central/Eastern Europe
XBB.1.5.55 ORF1a:T3356I, USA/Canada
HP.1 Alias of XBB.1.5.55.1, N:L13F, US/Mexico
HP.1.1 Alias of XBB.1.5.55.1.1, S:478R, Mexico
HP.1 Alias of XBB.1.5.55.1, N:L13F, US/Mexico From sars-cov-2-variants/lineage-proposals#277
HP.1.1 Alias of XBB.1.5.55.1.1, S:478R, Mexico From sars-cov-2-variants/lineage-proposals#277
XBB.1.5.56 S:A852S, USA
XBB.1.5.57 A20379G, C28312T, pre-T17124C, probable Spike-donor of XBL, #1973
XBB.1.5.58 S:704L, ORF1b:V1607I, ORF6:D6G, Guinea, from #1860
Expand All @@ -2784,7 +2784,7 @@ XBB.1.5.65 C583T, Germany
XBB.1.5.66 ORF1a:G519S, USA
XBB.1.5.67 C21691T, USA
XBB.1.5.68 S:P521T, ORF3a:L71I, C18501T, USA
HZ.1 Alias of XBB.1.5.68.1, S:K478R, 23266T, USA
HZ.1 Alias of XBB.1.5.68.1, S:K478R, 23266T, USA From sars-cov-2-variants/lineage-proposals#514
HZ.2 Alias of XBB.1.5.68.2, ORF1a:H3580Y, USA
HZ.3 Alias of XBB.1.5.68.3, ORF1a:I3693T, USA
XBB.1.5.69 ORF1a:V2943I,C22513T, USA
Expand Down Expand Up @@ -2839,7 +2839,7 @@ XBB.1.5.97 S:T941S, C7834T, New Zealand/Australia
XBB.1.5.98 S:E554K, ORF8:V32L, Ghana
XBB.1.5.99 ORF1a:V1122A, ORF1a:T2121I, Slovakia/Austria
XBB.1.5.100 S:V1122M, USA/Mexico
HY.1 Alias of XBB.1.5.100.1, S:478R, US/Mexico
HY.1 Alias of XBB.1.5.100.1, S:478R, US/Mexico From sars-cov-2-variants/lineage-proposals#453
XBB.1.5.101 ORF7a:E3Q, C14877T, Scandinavia/Poland/Vietnam
XBB.1.6 USA, S:L216F, S:H146K, from issue #1428
XBB.1.7 USA-NY, S:V608I
Expand Down Expand Up @@ -2947,7 +2947,7 @@ HK.2 Alias of XBB.1.9.2.5.1.1.2, S:Q14H, China From sars-cov-2-variants/lineage-
HK.3 Alias of XBB.1.9.2.5.1.1.3, S:L455F, China from https://github.com/sars-cov-2-variants/lineage-proposals/issues/414
HK.4 Alias of XBB.1.9.2.5.1.1.4, S:T883I, China
HK.5 Alias of XBB.1.9.2.5.1.1.5, S:Q677H, China
EG.5.1.2 Alias of XBB.1.9.2.5.1.2, Japan, ORF1b:V1644I
EG.5.1.2 Alias of XBB.1.9.2.5.1.2, Japan, ORF1b:V1644I From sars-cov-2-variants/lineage-proposals#301
EG.5.1.3 Alias of XBB.1.9.2.5.1.3, ORF1a:R542C, C22570T from https://github.com/sars-cov-2-variants/lineage-proposals/issues/222
EG.5.1.4 Alias of XBB.1.9.2.5.1.4, ORF1b:K2557R from https://github.com/cov-lineages/pango-designation/issues/2117
EG.5.1.5 Alias of XBB.1.9.2.5.1.5, ORF1a:L3293I, ORF1b:T1274I, ORF1b:L2349V, Portugal
Expand Down Expand Up @@ -2981,7 +2981,7 @@ XBB.1.11.1 Indonesia/Malaysia/Singapore, S:S486P，from #1490
FP.1 Alias of XBB.1.11.1.1, A6616G, C21642T, following ORF1a:T2016I, Singapore, from #1847
FP.2 Alias of XBB.1.11.1.2, S:F186S, ORF1a:V3078I, Indonesia/Malaysia/Singapore
FP.2.1 Alias of XBB.1.11.1.2.1, S:478R, ORF1a:I693T, ORF1a:T951A, ORF3a:W149C, Indonesia
FP.2.1.1 Alias of XBB.1.11.1.2.1.1, S:L452Q, USA/Austria
FP.2.1.1 Alias of XBB.1.11.1.2.1.1, S:L452Q, USA/Austria From sars-cov-2-variants/lineage-proposals#329
FP.2.1.2 Alias of XBB.1.11.1.2.1.2, S:P521S, Indonesia
FP.3 Alias of XBB.1.11.1.3, S:478R, Indonesia/Malaysia From #2021
FP.4 Alias of XBB.1.11.1.4, C3241T, C2536T, Vietnam/South Korea/Japan
Expand Down Expand Up @@ -3149,7 +3149,7 @@ XBB.2.3.3 S:182N, India/USA From #1810
GJ.1 Alias of XBB.2.3.3.1, found mainly in China and USA, from pango-designation issue #2005
GJ.1.1 Alias of XBB.2.3.3.1.1, S:A222V, N:R319H, ORF1a:V1915I From sars-cov-2-variants/lineage-proposals#109
GJ.1.2 Alias of XBB.2.3.3.1.2, ORF1b:V1110I, from #2059
GJ.1.2.1 Alias of XBB.2.3.3.1.2.1, S:N450D, Singapore/Thailand/South Korea/USA/Spain
GJ.1.2.1 Alias of XBB.2.3.3.1.2.1, S:N450D, Singapore/Thailand/South Korea/USA/Spain From sars-cov-2-variants/lineage-proposals#446
GJ.2 Alias of XBB.2.3.3.2, S:I1114S, Europe
GJ.3 Alias of XBB.2.3.3.3, ORF1a:P971S, ORF1b:V2371L
GJ.4 Alias of XBB.2.3.3.4, S:M153I
Expand Down Expand Up @@ -3217,8 +3217,8 @@ XBC.1.6.1 ORF8:P36L, Australia
GT.1 Alias of XBC.1.6.1.1, S:I105V, C28333T, Australia
XBC.1.6.2 ORF1a:D827N, Australia
XBC.1.6.3 N:A173V, Australia
HW.1 Alias of XBC.1.6.3.1, ORF1a:T1597I, ORF1a:A2123V, Australia
HW.1.1 Alias of XBC.1.6.3.1.1, S:N460H, T16242A, C22120T, USA/Ireland
HW.1 Alias of XBC.1.6.3.1, ORF1a:T1597I, ORF1a:A2123V, Australia From sars-cov-2-variants/lineage-proposals#71
HW.1.1 Alias of XBC.1.6.3.1.1, S:N460H, T16242A, C22120T, USA/Ireland From sars-cov-2-variants/lineage-proposals#452
XBC.1.6.4 ORF1a:V1117I, T20286C, Australia
XBC.1.7 S:478R, S:444T, Philippines/Australia/Hong Kong
XBC.2 Mostly Philippines, defined by S:K97R
Expand Down
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