From 371da2ddcc04e2d51e4be80359e9ba4a60241e04 Mon Sep 17 00:00:00 2001 From: aviczhl2 Date: Sun, 6 Aug 2023 11:52:24 +0800 Subject: [PATCH] add 9 autorefs to lineage_notes.txt --- automated-issue-ref.ipynb | 84 ++++++++++----------------------------- autoref/milestone_sub.txt | 10 +++++ autoref/missing_refs.txt | 45 +++++---------------- lineage_notes.txt | 18 ++++----- 4 files changed, 49 insertions(+), 108 deletions(-) diff --git a/automated-issue-ref.ipynb b/automated-issue-ref.ipynb index ece62766..216911b9 100755 --- a/automated-issue-ref.ipynb +++ b/automated-issue-ref.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "code", - "execution_count": 41, + "execution_count": 1, "id": "f64573a2", "metadata": {}, "outputs": [], @@ -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", @@ -47,7 +47,7 @@ }, { "cell_type": "code", - "execution_count": 16, + "execution_count": 2, "id": "769f2d32", "metadata": { "scrolled": false @@ -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" ] } ], @@ -165,7 +162,7 @@ }, { "cell_type": "code", - "execution_count": 39, + "execution_count": 3, "id": "88a367db", "metadata": {}, "outputs": [], @@ -212,7 +209,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": 4, "id": "f5b15585", "metadata": {}, "outputs": [], @@ -235,7 +232,7 @@ }, { "cell_type": "code", - "execution_count": 42, + "execution_count": 5, "id": "a56544a8", "metadata": {}, "outputs": [ @@ -243,55 +240,16 @@ "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" ] } ], @@ -358,7 +316,7 @@ }, { "cell_type": "code", - "execution_count": 43, + "execution_count": 6, "id": "1c9369e1", "metadata": {}, "outputs": [ @@ -366,8 +324,8 @@ "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" ] } ], @@ -405,7 +363,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 2, "id": "7756372f", "metadata": {}, "outputs": [], diff --git a/autoref/milestone_sub.txt b/autoref/milestone_sub.txt index 1ff6f408..08fc28ea 100755 --- a/autoref/milestone_sub.txt +++ b/autoref/milestone_sub.txt @@ -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 diff --git a/autoref/missing_refs.txt b/autoref/missing_refs.txt index 19ca666c..fa74bfa7 100755 --- a/autoref/missing_refs.txt +++ b/autoref/missing_refs.txt @@ -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 diff --git a/lineage_notes.txt b/lineage_notes.txt index fa20514a..5376fb0e 100644 --- a/lineage_notes.txt +++ b/lineage_notes.txt @@ -2766,8 +2766,8 @@ XBB.1.5.52 C3589T XBB.1.5.53 S:F140I, S:L582F, S:R403K, South Africa，from #1804 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 @@ -2781,7 +2781,7 @@ 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 @@ -2836,7 +2836,7 @@ 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.1.6 USA, S:L216F, S:H146K, from issue #1428 XBB.1.7 USA-NY, S:V608I XBB.1.8 Denmark, S:186insSGG, C3241T From #1455 @@ -2942,7 +2942,7 @@ 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 @@ -2974,7 +2974,7 @@ 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 @@ -3138,7 +3138,7 @@ 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 XBB.2.3.4 S:478Q, India, from #1822 @@ -3204,8 +3204,8 @@ 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