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Merge pull request cov-lineages#2338 from aviczhl2/master
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 add 2 refs from main page and 78 from lineage-proposal
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@AngieHinrichs
AngieHinrichs authored Oct 20, 2023
2 parents 9c676bd + e8e9c40 commit 8cee4af
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Showing 4 changed files with 351 additions and 135 deletions.
126 changes: 96 additions & 30 deletions automated-issue-ref.ipynb
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"processed 990 milestones\n",
"processed 1000 milestones\n",
"processed 1010 milestones\n",
"processed 1020 milestones\n"
"processed 1020 milestones\n",
"processed 1030 milestones\n",
"processed 1040 milestones\n",
"processed 1050 milestones\n",
"processed 1060 milestones\n",
"processed 1070 milestones\n",
"processed 1080 milestones\n",
"processed 1090 milestones\n",
"processed 1100 milestones\n",
"processed 1110 milestones\n"
]
}
],
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},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 3,
"id": "88a367db",
"metadata": {},
"outputs": [],
Expand Down Expand Up @@ -247,7 +256,7 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 4,
"id": "f5b15585",
"metadata": {},
"outputs": [],
Expand All @@ -270,37 +279,94 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 5,
"id": "a56544a8",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"['DV.7.1.1', 'sars-cov-2-variants/lineage-proposals#732']\n",
"['DV.7.1.2', '#2258']\n",
"['JP.1', 'sars-cov-2-variants/lineage-proposals#655']\n",
"['CH.1.1.32', '#2150']\n",
"['GK.2.1.1', 'sars-cov-2-variants/lineage-proposals#716']\n",
"['GK.2.3', 'sars-cov-2-variants/lineage-proposals#813']\n",
"['GK.4', '#2276']\n",
"['JD.1.1.1', 'sars-cov-2-variants/lineage-proposals#864']\n",
"['JD.1.1.2', 'sars-cov-2-variants/lineage-proposals#754']\n",
"['FL.1.6', 'sars-cov-2-variants/lineage-proposals#59']\n",
"['FL.15.1.1', 'sars-cov-2-variants/lineage-proposals#646']\n",
"['FL.15.2', 'sars-cov-2-variants/lineage-proposals#578']\n",
"['FL.20.2', 'sars-cov-2-variants/lineage-proposals#571']\n",
"['FL.32', 'sars-cov-2-variants/lineage-proposals#719']\n",
"['FL.32.1', 'sars-cov-2-variants/lineage-proposals#719']\n",
"['FL.33.1', 'sars-cov-2-variants/lineage-proposals#828']\n",
"['HK.3.3', 'sars-cov-2-variants/lineage-proposals#744']\n",
"['JG.3', '#2231']\n",
"['EG.5.1.8', 'sars-cov-2-variants/lineage-proposals#537']\n",
"['EG.6.1.1', 'sars-cov-2-variants/lineage-proposals#546']\n",
"['JM.1', 'sars-cov-2-variants/lineage-proposals#569']\n",
"['GW.5', '#2142']\n",
"['GS.5', 'sars-cov-2-variants/lineage-proposals#768']\n"
"['JV.1', 'sars-cov-2-variants/lineage-proposals#760']\n",
"['DV.7.1.3', 'sars-cov-2-variants/lineage-proposals#851']\n",
"['DV.7.1.5', 'sars-cov-2-variants/lineage-proposals#729']\n",
"['JN.3', 'sars-cov-2-variants/lineage-proposals#892']\n",
"['JQ.1', 'sars-cov-2-variants/lineage-proposals#906']\n",
"['JH.2', '#2068']\n",
"['FD.5.1', 'sars-cov-2-variants/lineage-proposals#385']\n",
"['GK.1.2.1', '#2314']\n",
"['GK.1.6', 'sars-cov-2-variants/lineage-proposals#643']\n",
"['GK.1.6.1', 'sars-cov-2-variants/lineage-proposals#643']\n",
"['GK.2.4', 'sars-cov-2-variants/lineage-proposals#823']\n",
"['GK.5', 'sars-cov-2-variants/lineage-proposals#736']\n",
"['GK.5.1', 'sars-cov-2-variants/lineage-proposals#736']\n",
"['GK.6', 'sars-cov-2-variants/lineage-proposals#715']\n",
"['GK.7', 'sars-cov-2-variants/lineage-proposals#907']\n",
"['GK.8', 'sars-cov-2-variants/lineage-proposals#909']\n",
"['GK.8.1', 'sars-cov-2-variants/lineage-proposals#909']\n",
"['GK.10', 'sars-cov-2-variants/lineage-proposals#761']\n",
"['GN.1.3', 'sars-cov-2-variants/lineage-proposals#816']\n",
"['JD.1.1.3', 'sars-cov-2-variants/lineage-proposals#896']\n",
"['KA.1', 'sars-cov-2-variants/lineage-proposals#822']\n",
"['JZ.1', 'sars-cov-2-variants/lineage-proposals#224']\n",
"['HN.2', 'sars-cov-2-variants/lineage-proposals#676']\n",
"['HN.2.1', 'sars-cov-2-variants/lineage-proposals#676']\n",
"['HN.3.1', 'sars-cov-2-variants/lineage-proposals#383']\n",
"['HN.5', 'sars-cov-2-variants/lineage-proposals#936']\n",
"['FL.13.4', 'sars-cov-2-variants/lineage-proposals#638']\n",
"['FL.13.4.1', 'sars-cov-2-variants/lineage-proposals#638']\n",
"['FL.13.5', 'sars-cov-2-variants/lineage-proposals#692']\n",
"['FL.23.2', 'sars-cov-2-variants/lineage-proposals#381']\n",
"['HK.1.2', 'sars-cov-2-variants/lineage-proposals#631']\n",
"['HK.2.1', 'sars-cov-2-variants/lineage-proposals#537']\n",
"['HK.3.4', 'sars-cov-2-variants/lineage-proposals#764']\n",
"['HK.3.5', 'sars-cov-2-variants/lineage-proposals#865']\n",
"['HK.3.6', 'sars-cov-2-variants/lineage-proposals#809']\n",
"['HK.3.7', 'sars-cov-2-variants/lineage-proposals#793']\n",
"['HK.11.1', 'sars-cov-2-variants/lineage-proposals#537']\n",
"['HK.13', 'sars-cov-2-variants/lineage-proposals#537']\n",
"['HK.13.2', 'sars-cov-2-variants/lineage-proposals#943']\n",
"['HK.14', 'sars-cov-2-variants/lineage-proposals#537']\n",
"['HK.15', 'sars-cov-2-variants/lineage-proposals#588']\n",
"['HK.16', 'sars-cov-2-variants/lineage-proposals#841']\n",
"['HK.18', 'sars-cov-2-variants/lineage-proposals#800']\n",
"['JG.3.1', 'sars-cov-2-variants/lineage-proposals#829']\n",
"['HV.1.1', 'sars-cov-2-variants/lineage-proposals#866']\n",
"['HV.1.3', 'sars-cov-2-variants/lineage-proposals#924']\n",
"['JR.1.1', 'sars-cov-2-variants/lineage-proposals#537']\n",
"['EG.6.1.2', 'sars-cov-2-variants/lineage-proposals#826']\n",
"['GA.4.1.3', 'sars-cov-2-variants/lineage-proposals#968']\n",
"['GA.4.3', 'sars-cov-2-variants/lineage-proposals#908']\n",
"['GA.7.1', 'sars-cov-2-variants/lineage-proposals#755']\n",
"['FE.1.1.5', 'sars-cov-2-variants/lineage-proposals#556']\n",
"['GW.5.3', 'sars-cov-2-variants/lineage-proposals#815']\n",
"['GW.5.3.1', 'sars-cov-2-variants/lineage-proposals#815']\n",
"['FY.1.4', 'sars-cov-2-variants/lineage-proposals#165']\n",
"['FY.5.1', 'sars-cov-2-variants/lineage-proposals#929']\n",
"['FY.5.1.1', 'sars-cov-2-variants/lineage-proposals#790']\n",
"['FY.6.2', 'sars-cov-2-variants/lineage-proposals#637']\n",
"['FY.8', 'sars-cov-2-variants/lineage-proposals#635']\n",
"['JC.2', 'sars-cov-2-variants/lineage-proposals#961']\n",
"['JC.5', 'sars-cov-2-variants/lineage-proposals#629']\n",
"['HH.2.1', 'sars-cov-2-variants/lineage-proposals#236']\n",
"['HH.5', 'sars-cov-2-variants/lineage-proposals#438']\n",
"['HH.6', 'sars-cov-2-variants/lineage-proposals#236']\n",
"['HH.8.1', 'sars-cov-2-variants/lineage-proposals#236']\n",
"['JE.1.1', 'sars-cov-2-variants/lineage-proposals#827']\n",
"['GJ.1.2.6', 'sars-cov-2-variants/lineage-proposals#726']\n",
"['GJ.1.2.7', 'sars-cov-2-variants/lineage-proposals#726']\n",
"['GJ.5', 'sars-cov-2-variants/lineage-proposals#429']\n",
"['GJ.5.1', 'sars-cov-2-variants/lineage-proposals#429']\n",
"['GJ.6', 'sars-cov-2-variants/lineage-proposals#675']\n",
"['GJ.7', 'sars-cov-2-variants/lineage-proposals#439']\n",
"['XBB.2.3.15', 'sars-cov-2-variants/lineage-proposals#722']\n",
"['JS.2', 'sars-cov-2-variants/lineage-proposals#722']\n",
"['XBB.2.3.18', 'sars-cov-2-variants/lineage-proposals#738']\n",
"['JY.1', 'sars-cov-2-variants/lineage-proposals#731']\n",
"['XBC.1.6.5', 'sars-cov-2-variants/lineage-proposals#479']\n",
"['JT.1', 'sars-cov-2-variants/lineage-proposals#203']\n",
"['XCZ', 'sars-cov-2-variants/lineage-proposals#839']\n",
"['XDB', 'sars-cov-2-variants/lineage-proposals#969']\n"
]
}
],
Expand Down Expand Up @@ -391,10 +457,10 @@
" linsp=data[i].split()\n",
" \n",
" if (len(linsp)>0) and (linsp[0] in missing_refs):\n",
" if \"From\" in data[i]:\n",
" data[i]=data[i].split(\" From\")[0]\n",
" if \"，from\" in data[i]:\n",
" data[i]=data[i].split(\", from\")[0]\n",
" upgrade_count+=1\n",
" data[i]=data[i].replace('\\n','')+\" From \"+missing_refs[linsp[0]]+'\\n'\n",
" data[i]=data[i].replace('\\n','')+\", from \"+missing_refs[linsp[0]]+'\\n'\n",
" if 'sars' in missing_refs[linsp[0]]:\n",
" sub_count+=1\n",
" else:\n",
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97 changes: 95 additions & 2 deletions autoref/milestone.txt
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Expand Up @@ -889,6 +889,10 @@
819 GK.4 GK.4
820 JG.3 JG.3
821 CH.1.1.32 CH.1.1.32
822 XCQ XCQ
823 XCR XCR
824 GK.1.2.1 GK.1.2.1
825 XCS XCS
sars#1 XCE XCE
sars#2 XCF XCF
sars#4 CM.7.1 CM.7.1+CM.7.1.1
Expand Down Expand Up @@ -1001,8 +1005,9 @@ sars#114 HK.3.3 HK.3.3
sars#115 FL.4.11 FL.4.11
sars#116 GJ.1.2.5 GJ.1.2.5
sars#117 HK.3.2 HK.3.2
sars#118 EG.5.1.8 EG.5.1.8
sars#119 GW.5.1.1 GW.5.1.1
sars#119 GW.5.1.1 GW.5.1.1+GK.1.6+GK.1.6.1
sars#119 GK.1.6 GW.5.1.1+GK.1.6+GK.1.6.1
sars#119 GK.1.6.1 GW.5.1.1+GK.1.6+GK.1.6.1
sars#120 DV.7.1.1 DV.7.1.1
sars#121 GK.2.3 GK.2.3
sars#122 JG.3 JG.3
Expand All @@ -1024,3 +1029,91 @@ sars#137 FL.36 FL.36
sars#138 FL.15.2 FL.15.2
sars#139 FL.15.1 FL.15.1+FL.15.1.1
sars#139 FL.15.1.1 FL.15.1+FL.15.1.1
sars#140 GJ.5 GJ.5+GJ.5.1
sars#140 GJ.5.1 GJ.5+GJ.5.1
sars#141 JE.1.1 JE.1.1
sars#142 GJ.1.2.6 GJ.1.2.6+GJ.1.2.7
sars#142 GJ.1.2.7 GJ.1.2.6+GJ.1.2.7
sars#143 JD.1.1.3 JD.1.1.3
sars#144 JQ.1 JQ.1
sars#146 BA.2.86.2 BA.2.86.2
sars#147 JN.2 JN.2
sars#148 JN.3 JN.3
sars#149 GK.2.4 GK.2.4
sars#150 EG.6.1.2 EG.6.1.2
sars#151 HV.1.1 HV.1.1
sars#152 HV.1.3 HV.1.3
sars#154 HK.13.2 HK.13.2
sars#156 HK.1.2 HK.1.2
sars#157 EG.5.1.8 EG.5.1.8+HK.13+HK.1.1+HK.14+JR.1.1+HK.2.1+HK.11.1
sars#157 HK.13 EG.5.1.8+HK.13+HK.1.1+HK.14+JR.1.1+HK.2.1+HK.11.1
sars#157 HK.1.1 EG.5.1.8+HK.13+HK.1.1+HK.14+JR.1.1+HK.2.1+HK.11.1
sars#157 HK.14 EG.5.1.8+HK.13+HK.1.1+HK.14+JR.1.1+HK.2.1+HK.11.1
sars#157 JR.1.1 EG.5.1.8+HK.13+HK.1.1+HK.14+JR.1.1+HK.2.1+HK.11.1
sars#157 HK.2.1 EG.5.1.8+HK.13+HK.1.1+HK.14+JR.1.1+HK.2.1+HK.11.1
sars#157 HK.11.1 EG.5.1.8+HK.13+HK.1.1+HK.14+JR.1.1+HK.2.1+HK.11.1
sars#158 HK.15 HK.15
sars#159 GA.4.3 GA.4.3
sars#160 HK.16 HK.16
sars#161 HK.18 HK.18
sars#162 XBB.2.3.15 XBB.2.3.15+JS.2
sars#162 JS.2 XBB.2.3.15+JS.2
sars#163 GW.5.3 GW.5.3+GW.5.3.1
sars#163 GW.5.3.1 GW.5.3+GW.5.3.1
sars#164 JT.1 JT.1
sars#165 XBC.1.6.5 XBC.1.6.5
sars#167 GK.6 GK.6
sars#168 GK.7 GK.7
sars#170 GK.8 GK.8+GK.8.1
sars#170 GK.8.1 GK.8+GK.8.1
sars#171 GK.5 GK.5+GK.5.1
sars#171 GK.5.1 GK.5+GK.5.1
sars#172 GK.10 GK.10
sars#173 XBB.2.3.18 XBB.2.3.18
sars#174 GJ.6 GJ.6
sars#175 GJ.7 GJ.7
sars#176 JV.1 JV.1
sars#177 JC.2 JC.2
sars#178 JC.5 JC.5
sars#179 FL..30.1 FL..30.1
sars#180 FL.13.4 FL.13.4+FL.13.4.1
sars#180 FL.13.4.1 FL.13.4+FL.13.4.1
sars#181 FL.13.5 FL.13.5
sars#182 DV.7.1.3 DV.7.1.3
sars#183 DV.7.1.5 DV.7.1.5
sars#184 XCT XCT
sars#185 FL.23.2 FL.23.2
sars#186 XCU XCU
sars#187 HH.2.1 HH.2.1+HH.6+HH.8.1
sars#187 HH.6 HH.2.1+HH.6+HH.8.1
sars#187 HH.8.1 HH.2.1+HH.6+HH.8.1
sars#188 JY.1 JY.1
sars#189 JG.3.1 JG.3.1
sars#190 HK.3.4 HK.3.4
sars#191 HK.3.5 HK.3.5
sars#192 HK.3.6 HK.3.6
sars#193 HK.3.7 HK.3.7
sars#194 GA.7.1 GA.7.1
sars#195 XCV XCV
sars#196 XBB.2.3.20 XBB.2.3.20
sars#197 JZ.1 JZ.1
sars#198 FD.5.1 FD.5.1
sars#199 KA.1 KA.1
sars#200 GN.1.3 GN.1.3
sars#201 XCY XCY
sars#202 XCZ XCZ
sars#203 FE.1.1.5 FE.1.1.5
sars#204 HN.5 HN.5
sars#206 HN.3.1 HN.3.1
sars#207 FY.8 FY.8
sars#208 FY.6.2 FY.6.2
sars#209 FY.1.4 FY.1.4
sars#211 FY.5.1 FY.5.1
sars#212 FY.5.1.1 FY.5.1.1
sars#213 HN.2 HN.2+HN.2.1
sars#213 HN.2.1 HN.2+HN.2.1
sars#214 GA.4.1.3 GA.4.1.3
sars#215 XDA XDA
sars#216 XDB XDB
sars#217 XDC XDC
sars#218 HH.5 HH.5
103 changes: 80 additions & 23 deletions autoref/missing_refs.txt
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@@ -1,23 +1,80 @@
DV.7.1.1 sars-cov-2-variants/lineage-proposals#732
DV.7.1.2 #2258
JP.1 sars-cov-2-variants/lineage-proposals#655
CH.1.1.32 #2150
GK.2.1.1 sars-cov-2-variants/lineage-proposals#716
GK.2.3 sars-cov-2-variants/lineage-proposals#813
GK.4 #2276
JD.1.1.1 sars-cov-2-variants/lineage-proposals#864
JD.1.1.2 sars-cov-2-variants/lineage-proposals#754
FL.1.6 sars-cov-2-variants/lineage-proposals#59
FL.15.1.1 sars-cov-2-variants/lineage-proposals#646
FL.15.2 sars-cov-2-variants/lineage-proposals#578
FL.20.2 sars-cov-2-variants/lineage-proposals#571
FL.32 sars-cov-2-variants/lineage-proposals#719
FL.32.1 sars-cov-2-variants/lineage-proposals#719
FL.33.1 sars-cov-2-variants/lineage-proposals#828
HK.3.3 sars-cov-2-variants/lineage-proposals#744
JG.3 #2231
EG.5.1.8 sars-cov-2-variants/lineage-proposals#537
EG.6.1.1 sars-cov-2-variants/lineage-proposals#546
JM.1 sars-cov-2-variants/lineage-proposals#569
GW.5 #2142
GS.5 sars-cov-2-variants/lineage-proposals#768
JV.1 sars-cov-2-variants/lineage-proposals#760
DV.7.1.3 sars-cov-2-variants/lineage-proposals#851
DV.7.1.5 sars-cov-2-variants/lineage-proposals#729
JN.3 sars-cov-2-variants/lineage-proposals#892
JQ.1 sars-cov-2-variants/lineage-proposals#906
JH.2 #2068
FD.5.1 sars-cov-2-variants/lineage-proposals#385
GK.1.2.1 #2314
GK.1.6 sars-cov-2-variants/lineage-proposals#643
GK.1.6.1 sars-cov-2-variants/lineage-proposals#643
GK.2.4 sars-cov-2-variants/lineage-proposals#823
GK.5 sars-cov-2-variants/lineage-proposals#736
GK.5.1 sars-cov-2-variants/lineage-proposals#736
GK.6 sars-cov-2-variants/lineage-proposals#715
GK.7 sars-cov-2-variants/lineage-proposals#907
GK.8 sars-cov-2-variants/lineage-proposals#909
GK.8.1 sars-cov-2-variants/lineage-proposals#909
GK.10 sars-cov-2-variants/lineage-proposals#761
GN.1.3 sars-cov-2-variants/lineage-proposals#816
JD.1.1.3 sars-cov-2-variants/lineage-proposals#896
KA.1 sars-cov-2-variants/lineage-proposals#822
JZ.1 sars-cov-2-variants/lineage-proposals#224
HN.2 sars-cov-2-variants/lineage-proposals#676
HN.2.1 sars-cov-2-variants/lineage-proposals#676
HN.3.1 sars-cov-2-variants/lineage-proposals#383
HN.5 sars-cov-2-variants/lineage-proposals#936
FL.13.4 sars-cov-2-variants/lineage-proposals#638
FL.13.4.1 sars-cov-2-variants/lineage-proposals#638
FL.13.5 sars-cov-2-variants/lineage-proposals#692
FL.23.2 sars-cov-2-variants/lineage-proposals#381
HK.1.2 sars-cov-2-variants/lineage-proposals#631
HK.2.1 sars-cov-2-variants/lineage-proposals#537
HK.3.4 sars-cov-2-variants/lineage-proposals#764
HK.3.5 sars-cov-2-variants/lineage-proposals#865
HK.3.6 sars-cov-2-variants/lineage-proposals#809
HK.3.7 sars-cov-2-variants/lineage-proposals#793
HK.11.1 sars-cov-2-variants/lineage-proposals#537
HK.13 sars-cov-2-variants/lineage-proposals#537
HK.13.2 sars-cov-2-variants/lineage-proposals#943
HK.14 sars-cov-2-variants/lineage-proposals#537
HK.15 sars-cov-2-variants/lineage-proposals#588
HK.16 sars-cov-2-variants/lineage-proposals#841
HK.18 sars-cov-2-variants/lineage-proposals#800
JG.3.1 sars-cov-2-variants/lineage-proposals#829
HV.1.1 sars-cov-2-variants/lineage-proposals#866
HV.1.3 sars-cov-2-variants/lineage-proposals#924
JR.1.1 sars-cov-2-variants/lineage-proposals#537
EG.6.1.2 sars-cov-2-variants/lineage-proposals#826
GA.4.1.3 sars-cov-2-variants/lineage-proposals#968
GA.4.3 sars-cov-2-variants/lineage-proposals#908
GA.7.1 sars-cov-2-variants/lineage-proposals#755
FE.1.1.5 sars-cov-2-variants/lineage-proposals#556
GW.5.3 sars-cov-2-variants/lineage-proposals#815
GW.5.3.1 sars-cov-2-variants/lineage-proposals#815
FY.1.4 sars-cov-2-variants/lineage-proposals#165
FY.5.1 sars-cov-2-variants/lineage-proposals#929
FY.5.1.1 sars-cov-2-variants/lineage-proposals#790
FY.6.2 sars-cov-2-variants/lineage-proposals#637
FY.8 sars-cov-2-variants/lineage-proposals#635
JC.2 sars-cov-2-variants/lineage-proposals#961
JC.5 sars-cov-2-variants/lineage-proposals#629
HH.2.1 sars-cov-2-variants/lineage-proposals#236
HH.5 sars-cov-2-variants/lineage-proposals#438
HH.6 sars-cov-2-variants/lineage-proposals#236
HH.8.1 sars-cov-2-variants/lineage-proposals#236
JE.1.1 sars-cov-2-variants/lineage-proposals#827
GJ.1.2.6 sars-cov-2-variants/lineage-proposals#726
GJ.1.2.7 sars-cov-2-variants/lineage-proposals#726
GJ.5 sars-cov-2-variants/lineage-proposals#429
GJ.5.1 sars-cov-2-variants/lineage-proposals#429
GJ.6 sars-cov-2-variants/lineage-proposals#675
GJ.7 sars-cov-2-variants/lineage-proposals#439
XBB.2.3.15 sars-cov-2-variants/lineage-proposals#722
JS.2 sars-cov-2-variants/lineage-proposals#722
XBB.2.3.18 sars-cov-2-variants/lineage-proposals#738
JY.1 sars-cov-2-variants/lineage-proposals#731
XBC.1.6.5 sars-cov-2-variants/lineage-proposals#479
JT.1 sars-cov-2-variants/lineage-proposals#203
XCZ sars-cov-2-variants/lineage-proposals#839
XDB sars-cov-2-variants/lineage-proposals#969
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