From bda0bb04cf28706d2c7f8cf190fda25feec105ff Mon Sep 17 00:00:00 2001 From: ishanu Date: Wed, 18 Oct 2023 13:41:50 -0500 Subject: [PATCH] upd --- .../rbd_distance_baseline_predictor.ipynb | 1592 +++++++++++++++++ 1 file changed, 1592 insertions(+) create mode 100644 extras/baseline/rbd_distance_baseline_predictor.ipynb diff --git a/extras/baseline/rbd_distance_baseline_predictor.ipynb b/extras/baseline/rbd_distance_baseline_predictor.ipynb new file mode 100644 index 00000000..3b89e8c6 --- /dev/null +++ b/extras/baseline/rbd_distance_baseline_predictor.ipynb @@ -0,0 +1,1592 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "id": "4c34e438", + "metadata": {}, + "outputs": [], + "source": [ + "import pandas as pd\n", + "import numpy as np" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "c92f77bd", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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subtypeha_accessionna_accessionhanaha_riskna_riskgeometric_mean_riskemergence_riskemergence_risk_varimpact_riskimpact_risk_varis_irat
id
A/swine/Shandong/1207/2016H1N1EPI1751427EPI1751500MEARLFVLFCAFTTLKADTICVGYHANNSTDTVDTILEKNVTVTHS...MNPNQKIITIGSICMTIGIASLILQIGNIISIWISHSIQIENQNQS...[0.059268942695459764, 0.059207549599012387, 0...[0.04153677158036683, 0.04121188550974603, 0.0...[0.04961693798040306, 0.04939691038300986, 0.0...7.50.0018616.90.0000031.0
A/Ohio/13/2017H3N2EPI1056653EPI1056652MKTIIALSHILCLVFAQKLPGNDNNMATLCLGHHAVPNGTIVKTIT...MNPNQKIITIGSVSLIIATICFLMQIAILVTTITLHFKQHNCDSSP...[0.007443436845452373, 0.007528108280118501, 0...[0.0684551151913223, 0.06848866622907772, 0.06...[0.02257302209884124, 0.0227066090672604, 0.02...6.60.0719315.80.0039411.0
A/Hong Kong/125/2017H7N9EPI977395EPI977394MNTQILVFALIAIIPTNADKICLGHHAVSNGTKVNTLTERGVEVVN...MNPNQKILCTSATAITIGAIAVLIGIANLGLNIGLHLKPGCNCSHS...[0.008053012400112526, 0.011702039255706398, 0...[0.001702640937331002, 0.0015986998079791897, ...[0.0037028892207661, 0.004325280096255358, 0.0...6.50.0577407.50.0025931.0
A/Shanghai/02/2013H7N9EPI448936EPI448938MNTQILVFALIAIIPTNADKICLGHHAVSNGTKVNTLTERGVEVVN...MNPNQKILCTSATAIIIGAIAVLIGMANLGLNIGLHLKPGCNCSHS...[0.0029756019607934496, 0.003893470493957003, ...[0.0014946170772583095, 0.0014623661892494138,...[0.00210888252534967, 0.002386143249933443, 0....6.40.0257697.20.0005181.0
A/Anhui-Lujiang/39/2018H9N2EPI1315830EPI1315828METVSLITILLVATASNADKICIGYQSTNSTETVDTLTENNVPVTH...MNPNQKITAIGSVSLIIAIICLLMQIAILTTTMTLHFGQKECSNPS...[0.013913606506215747, 0.014682700295856159, 0...[0.025868069685588593, 0.04350993746295142, 0....[0.018971508708604274, 0.025275351068975476, 0...6.20.1344405.90.0138571.0
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" + ], + "text/plain": [ + " subtype ha_accession na_accession \\\n", + "id \n", + "A/swine/Shandong/1207/2016 H1N1 EPI1751427 EPI1751500 \n", + "A/Ohio/13/2017 H3N2 EPI1056653 EPI1056652 \n", + "A/Hong Kong/125/2017 H7N9 EPI977395 EPI977394 \n", + "A/Shanghai/02/2013 H7N9 EPI448936 EPI448938 \n", + "A/Anhui-Lujiang/39/2018 H9N2 EPI1315830 EPI1315828 \n", + "\n", + " ha \\\n", + "id \n", + "A/swine/Shandong/1207/2016 MEARLFVLFCAFTTLKADTICVGYHANNSTDTVDTILEKNVTVTHS... \n", + "A/Ohio/13/2017 MKTIIALSHILCLVFAQKLPGNDNNMATLCLGHHAVPNGTIVKTIT... \n", + "A/Hong Kong/125/2017 MNTQILVFALIAIIPTNADKICLGHHAVSNGTKVNTLTERGVEVVN... \n", + "A/Shanghai/02/2013 MNTQILVFALIAIIPTNADKICLGHHAVSNGTKVNTLTERGVEVVN... \n", + "A/Anhui-Lujiang/39/2018 METVSLITILLVATASNADKICIGYQSTNSTETVDTLTENNVPVTH... \n", + "\n", + " na \\\n", + "id \n", + "A/swine/Shandong/1207/2016 MNPNQKIITIGSICMTIGIASLILQIGNIISIWISHSIQIENQNQS... \n", + "A/Ohio/13/2017 MNPNQKIITIGSVSLIIATICFLMQIAILVTTITLHFKQHNCDSSP... \n", + "A/Hong Kong/125/2017 MNPNQKILCTSATAITIGAIAVLIGIANLGLNIGLHLKPGCNCSHS... \n", + "A/Shanghai/02/2013 MNPNQKILCTSATAIIIGAIAVLIGMANLGLNIGLHLKPGCNCSHS... \n", + "A/Anhui-Lujiang/39/2018 MNPNQKITAIGSVSLIIAIICLLMQIAILTTTMTLHFGQKECSNPS... \n", + "\n", + " ha_risk \\\n", + "id \n", + "A/swine/Shandong/1207/2016 [0.059268942695459764, 0.059207549599012387, 0... \n", + "A/Ohio/13/2017 [0.007443436845452373, 0.007528108280118501, 0... \n", + "A/Hong Kong/125/2017 [0.008053012400112526, 0.011702039255706398, 0... \n", + "A/Shanghai/02/2013 [0.0029756019607934496, 0.003893470493957003, ... \n", + "A/Anhui-Lujiang/39/2018 [0.013913606506215747, 0.014682700295856159, 0... \n", + "\n", + " na_risk \\\n", + "id \n", + "A/swine/Shandong/1207/2016 [0.04153677158036683, 0.04121188550974603, 0.0... \n", + "A/Ohio/13/2017 [0.0684551151913223, 0.06848866622907772, 0.06... \n", + "A/Hong Kong/125/2017 [0.001702640937331002, 0.0015986998079791897, ... \n", + "A/Shanghai/02/2013 [0.0014946170772583095, 0.0014623661892494138,... \n", + "A/Anhui-Lujiang/39/2018 [0.025868069685588593, 0.04350993746295142, 0.... \n", + "\n", + " geometric_mean_risk \\\n", + "id \n", + "A/swine/Shandong/1207/2016 [0.04961693798040306, 0.04939691038300986, 0.0... \n", + "A/Ohio/13/2017 [0.02257302209884124, 0.0227066090672604, 0.02... \n", + "A/Hong Kong/125/2017 [0.0037028892207661, 0.004325280096255358, 0.0... \n", + "A/Shanghai/02/2013 [0.00210888252534967, 0.002386143249933443, 0.... \n", + "A/Anhui-Lujiang/39/2018 [0.018971508708604274, 0.025275351068975476, 0... \n", + "\n", + " emergence_risk emergence_risk_var impact_risk \\\n", + "id \n", + "A/swine/Shandong/1207/2016 7.5 0.001861 6.9 \n", + "A/Ohio/13/2017 6.6 0.071931 5.8 \n", + "A/Hong Kong/125/2017 6.5 0.057740 7.5 \n", + "A/Shanghai/02/2013 6.4 0.025769 7.2 \n", + "A/Anhui-Lujiang/39/2018 6.2 0.134440 5.9 \n", + "\n", + " impact_risk_var is_irat \n", + "id \n", + "A/swine/Shandong/1207/2016 0.000003 1.0 \n", + "A/Ohio/13/2017 0.003941 1.0 \n", + "A/Hong Kong/125/2017 0.002593 1.0 \n", + "A/Shanghai/02/2013 0.000518 1.0 \n", + "A/Anhui-Lujiang/39/2018 0.013857 1.0 " + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "PATH='../../paper_data_v2/irat_enet/results/animal_predictions/combined_results_with_irat.csv'\n", + "df=pd.read_csv(PATH,index_col=0)\n", + "df.head()" + ] + }, + { + "cell_type": "code", + "execution_count": 95, + "id": "cf9b9f93", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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emergence_riskimpact_riskis_iratha_riskgeometric_mean_risk
id
A/swine/Shandong/1207/20167.56.91.0[0.059268942695459764, 0.059207549599012387, 0...[0.04961693798040306, 0.04939691038300986, 0.0...
A/Ohio/13/20176.65.81.0[0.007443436845452373, 0.007528108280118501, 0...[0.02257302209884124, 0.0227066090672604, 0.02...
A/Hong Kong/125/20176.57.51.0[0.008053012400112526, 0.011702039255706398, 0...[0.0037028892207661, 0.004325280096255358, 0.0...
A/Shanghai/02/20136.47.21.0[0.0029756019607934496, 0.003893470493957003, ...[0.00210888252534967, 0.002386143249933443, 0....
A/Anhui-Lujiang/39/20186.25.91.0[0.013913606506215747, 0.014682700295856159, 0...[0.018971508708604274, 0.025275351068975476, 0...
A/Indiana/08/20116.04.51.0[0.015833187603574352, 0.01579698562348106, 0....[0.016902504332314258, 0.01683599355230769, 0....
A/California/62/20185.85.71.0[0.25421003694129446, 0.17137241238504203, 0.1...[0.11064301441040252, 0.08010185536798671, 0.0...
A/Bangladesh/0994/20115.65.41.0[0.047962278609110426, 0.047376021553330504, 0...[0.1509708016952567, 0.14755990149418968, 0.15...
A/Sichuan/06681/20215.36.31.0[0.3401659563640977, 0.4372884849313668, 0.335...[0.14098323610429828, 0.16479919492131653, 0.1...
A/Vietnam/1203/20045.26.61.0[0.12775494527491757, 0.11190370497308454, 0.1...[0.07357578392227798, 0.06512340773617227, 0.0...
A/Yunnan/14564/20155.06.61.0[0.20080863109685176, 0.10301992847449411, 0.2...[0.08744456695565636, 0.05634300538887098, 0.0...
A/Astrakhan/3212/20204.65.21.0[0.2452941610025089, 0.2335184366024988, 0.221...[0.3660547134708487, 0.352999397804964, 0.3433...
A/Netherlands/219/20034.65.81.0[0.16431983904493178, 0.16426481855673325, 0.1...[0.2735882731677115, 0.27353672735391277, 0.27...
A/American wigeon/South Carolina/AH0195145/20214.45.11.0[0.22507345650411203, 0.253385372610634, 0.250...[0.2618009640888491, 0.28041946959711944, 0.27...
A/Jiangxi-Donghu/346/20134.36.01.0[0.03929273071556801, 0.3559593557688923, 0.15...[0.027090727115239115, 0.1774459269887038, 0.0...
A/gyrfalcon/Washington/41088/20144.24.61.0[0.24718594726896237, 0.2361702553946631, 0.22...[0.36678073190475535, 0.35436513753260845, 0.3...
A/Northern pintail/Washington/40964/20143.84.11.0[0.2410948922603147, 0.22971447028474637, 0.21...[0.349366042786461, 0.34039602323151935, 0.331...
A/canine/Illinois/12191/20153.73.71.0[0.01616230298118454, 0.016067588755834316, 0....[0.024453287740176615, 0.024374121053616235, 0...
A/American green-winged teal/Washington/1957050/20143.64.11.0[0.22532859992890514, 0.2523992705219045, 0.24...[0.2592089036823605, 0.2766319981079351, 0.273...
A/turkey/Indiana/1573-2/20163.43.91.0[0.042531258378212616, 0.046850178126532895, 0...[0.13246011857462825, 0.13903537495472926, 0.1...
A/chicken/Tennessee/17-007431-3/20173.13.51.0[0.032175814200484966, 0.03682965073244792, 0....[0.12816247069024164, 0.1371356157354049, 0.12...
A/chicken/Tennessee/17-007147-2/20172.83.51.0[0.082518541655176, 0.08595812903880762, 0.083...[0.20524466180722442, 0.20950526315825033, 0.2...
\n", + "
" + ], + "text/plain": [ + " emergence_risk \\\n", + "id \n", + "A/swine/Shandong/1207/2016 7.5 \n", + "A/Ohio/13/2017 6.6 \n", + "A/Hong Kong/125/2017 6.5 \n", + "A/Shanghai/02/2013 6.4 \n", + "A/Anhui-Lujiang/39/2018 6.2 \n", + "A/Indiana/08/2011 6.0 \n", + "A/California/62/2018 5.8 \n", + "A/Bangladesh/0994/2011 5.6 \n", + "A/Sichuan/06681/2021 5.3 \n", + "A/Vietnam/1203/2004 5.2 \n", + "A/Yunnan/14564/2015 5.0 \n", + "A/Astrakhan/3212/2020 4.6 \n", + "A/Netherlands/219/2003 4.6 \n", + "A/American wigeon/South Carolina/AH0195145/2021 4.4 \n", + "A/Jiangxi-Donghu/346/2013 4.3 \n", + "A/gyrfalcon/Washington/41088/2014 4.2 \n", + "A/Northern pintail/Washington/40964/2014 3.8 \n", + "A/canine/Illinois/12191/2015 3.7 \n", + "A/American green-winged teal/Washington/1957050... 3.6 \n", + "A/turkey/Indiana/1573-2/2016 3.4 \n", + "A/chicken/Tennessee/17-007431-3/2017 3.1 \n", + "A/chicken/Tennessee/17-007147-2/2017 2.8 \n", + "\n", + " impact_risk is_irat \\\n", + "id \n", + "A/swine/Shandong/1207/2016 6.9 1.0 \n", + "A/Ohio/13/2017 5.8 1.0 \n", + "A/Hong Kong/125/2017 7.5 1.0 \n", + "A/Shanghai/02/2013 7.2 1.0 \n", + "A/Anhui-Lujiang/39/2018 5.9 1.0 \n", + "A/Indiana/08/2011 4.5 1.0 \n", + "A/California/62/2018 5.7 1.0 \n", + "A/Bangladesh/0994/2011 5.4 1.0 \n", + "A/Sichuan/06681/2021 6.3 1.0 \n", + "A/Vietnam/1203/2004 6.6 1.0 \n", + "A/Yunnan/14564/2015 6.6 1.0 \n", + "A/Astrakhan/3212/2020 5.2 1.0 \n", + "A/Netherlands/219/2003 5.8 1.0 \n", + "A/American wigeon/South Carolina/AH0195145/2021 5.1 1.0 \n", + "A/Jiangxi-Donghu/346/2013 6.0 1.0 \n", + "A/gyrfalcon/Washington/41088/2014 4.6 1.0 \n", + "A/Northern pintail/Washington/40964/2014 4.1 1.0 \n", + "A/canine/Illinois/12191/2015 3.7 1.0 \n", + "A/American green-winged teal/Washington/1957050... 4.1 1.0 \n", + "A/turkey/Indiana/1573-2/2016 3.9 1.0 \n", + "A/chicken/Tennessee/17-007431-3/2017 3.5 1.0 \n", + "A/chicken/Tennessee/17-007147-2/2017 3.5 1.0 \n", + "\n", + " ha_risk \\\n", + "id \n", + "A/swine/Shandong/1207/2016 [0.059268942695459764, 0.059207549599012387, 0... \n", + "A/Ohio/13/2017 [0.007443436845452373, 0.007528108280118501, 0... \n", + "A/Hong Kong/125/2017 [0.008053012400112526, 0.011702039255706398, 0... \n", + "A/Shanghai/02/2013 [0.0029756019607934496, 0.003893470493957003, ... \n", + "A/Anhui-Lujiang/39/2018 [0.013913606506215747, 0.014682700295856159, 0... \n", + "A/Indiana/08/2011 [0.015833187603574352, 0.01579698562348106, 0.... \n", + "A/California/62/2018 [0.25421003694129446, 0.17137241238504203, 0.1... \n", + "A/Bangladesh/0994/2011 [0.047962278609110426, 0.047376021553330504, 0... \n", + "A/Sichuan/06681/2021 [0.3401659563640977, 0.4372884849313668, 0.335... \n", + "A/Vietnam/1203/2004 [0.12775494527491757, 0.11190370497308454, 0.1... \n", + "A/Yunnan/14564/2015 [0.20080863109685176, 0.10301992847449411, 0.2... \n", + "A/Astrakhan/3212/2020 [0.2452941610025089, 0.2335184366024988, 0.221... \n", + "A/Netherlands/219/2003 [0.16431983904493178, 0.16426481855673325, 0.1... \n", + "A/American wigeon/South Carolina/AH0195145/2021 [0.22507345650411203, 0.253385372610634, 0.250... \n", + "A/Jiangxi-Donghu/346/2013 [0.03929273071556801, 0.3559593557688923, 0.15... \n", + "A/gyrfalcon/Washington/41088/2014 [0.24718594726896237, 0.2361702553946631, 0.22... \n", + "A/Northern pintail/Washington/40964/2014 [0.2410948922603147, 0.22971447028474637, 0.21... \n", + "A/canine/Illinois/12191/2015 [0.01616230298118454, 0.016067588755834316, 0.... \n", + "A/American green-winged teal/Washington/1957050... [0.22532859992890514, 0.2523992705219045, 0.24... \n", + "A/turkey/Indiana/1573-2/2016 [0.042531258378212616, 0.046850178126532895, 0... \n", + "A/chicken/Tennessee/17-007431-3/2017 [0.032175814200484966, 0.03682965073244792, 0.... \n", + "A/chicken/Tennessee/17-007147-2/2017 [0.082518541655176, 0.08595812903880762, 0.083... \n", + "\n", + " geometric_mean_risk \n", + "id \n", + "A/swine/Shandong/1207/2016 [0.04961693798040306, 0.04939691038300986, 0.0... \n", + "A/Ohio/13/2017 [0.02257302209884124, 0.0227066090672604, 0.02... \n", + "A/Hong Kong/125/2017 [0.0037028892207661, 0.004325280096255358, 0.0... \n", + "A/Shanghai/02/2013 [0.00210888252534967, 0.002386143249933443, 0.... \n", + "A/Anhui-Lujiang/39/2018 [0.018971508708604274, 0.025275351068975476, 0... \n", + "A/Indiana/08/2011 [0.016902504332314258, 0.01683599355230769, 0.... \n", + "A/California/62/2018 [0.11064301441040252, 0.08010185536798671, 0.0... \n", + "A/Bangladesh/0994/2011 [0.1509708016952567, 0.14755990149418968, 0.15... \n", + "A/Sichuan/06681/2021 [0.14098323610429828, 0.16479919492131653, 0.1... \n", + "A/Vietnam/1203/2004 [0.07357578392227798, 0.06512340773617227, 0.0... \n", + "A/Yunnan/14564/2015 [0.08744456695565636, 0.05634300538887098, 0.0... \n", + "A/Astrakhan/3212/2020 [0.3660547134708487, 0.352999397804964, 0.3433... \n", + "A/Netherlands/219/2003 [0.2735882731677115, 0.27353672735391277, 0.27... \n", + "A/American wigeon/South Carolina/AH0195145/2021 [0.2618009640888491, 0.28041946959711944, 0.27... \n", + "A/Jiangxi-Donghu/346/2013 [0.027090727115239115, 0.1774459269887038, 0.0... \n", + "A/gyrfalcon/Washington/41088/2014 [0.36678073190475535, 0.35436513753260845, 0.3... \n", + "A/Northern pintail/Washington/40964/2014 [0.349366042786461, 0.34039602323151935, 0.331... \n", + "A/canine/Illinois/12191/2015 [0.024453287740176615, 0.024374121053616235, 0... \n", + "A/American green-winged teal/Washington/1957050... [0.2592089036823605, 0.2766319981079351, 0.273... \n", + "A/turkey/Indiana/1573-2/2016 [0.13246011857462825, 0.13903537495472926, 0.1... \n", + "A/chicken/Tennessee/17-007431-3/2017 [0.12816247069024164, 0.1371356157354049, 0.12... \n", + "A/chicken/Tennessee/17-007147-2/2017 [0.20524466180722442, 0.20950526315825033, 0.2... " + ] + }, + "execution_count": 95, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "df_h1n1=df#[df.subtype=='H1N1']\n", + "df_=df_h1n1[['emergence_risk','impact_risk','is_irat','ha_risk','geometric_mean_risk']]\n", + "df_[df_.is_irat==1]" + ] + }, + { + "cell_type": "code", + "execution_count": 94, + "id": "523e82f7", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "Index(['subtype', 'ha_accession', 'na_accession', 'ha', 'na', 'ha_risk',\n", + " 'na_risk', 'geometric_mean_risk', 'emergence_risk',\n", + " 'emergence_risk_var', 'impact_risk', 'impact_risk_var', 'is_irat'],\n", + " dtype='object')" + ] + }, + "execution_count": 94, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "df.columns" + ] + }, + { + "cell_type": "code", + "execution_count": 107, + "id": "be2e6e33", + "metadata": {}, + "outputs": [], + "source": [ + "RBD=range(63,286)\n", + "R=range(150,236)\n", + "R=range(50,336)\n", + "RBD=range(90,240)\n", + "binding_pocket=range(190,200)\n", + "\n", + "R=[90, 91,92,93,94,155,156,157,158,159,160,190,191,192,193,194,195,220,221,222,223,224,225,226]\n", + "df_['frag_rbd']=[''.join(np.array(list(x))[RBD]) for x in df_h1n1.ha.values]\n", + "df_['frag_sel']=[''.join(np.array(list(x))[R]) for x in df_h1n1.ha.values]\n", + "df_['frag_pocket']=[''.join(np.array(list(x))[binding_pocket]) for x in df_h1n1.ha.values]\n", + "df_['mean_geom_risk'] = [np.array(eval(x)).mean() for x in df_.geometric_mean_risk]\n", + "df_['mean_ha_risk'] = [np.array(eval(x)).mean() for x in df_.ha_risk]\n", + "df_['max_ha_risk'] = [np.array(eval(x)).max() for x in df_.ha_risk]\n", + "df_['min_ha_risk'] = [np.array(eval(x)).min() for x in df_.ha_risk]" + ] + }, + { + "cell_type": "code", + "execution_count": 108, + "id": "f424b5a0", + "metadata": {}, + "outputs": [], + "source": [ + "seq0=['MKAILVVLLYTFTTANADTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTARSWSYIVETSNSDNGTCYPGDFINYEELREQLSSVSSFERFEIFPKTSSWPNHDSDKGVTAACPHAGAKSFYKNLIWLVKKGNSYPKLNQTYINDKGKEVLVLWGIHHPPTIAAQESLYQNADAYVFVGTSRYSKKFKPEIATRPKVRDQEGRMNYYWTLVEPGDKITFEATGNLVVPRYAFTMERDAGSGIIISDTPVHDCNTTCQTPEGAINTSLPFQNVHPITIGKC\\PKYVKSTKLRLATGLRNVPSIQSRGLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDKITNKVNSVIEKMNTQFTAVGKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRNQLKNNAKEIGNG\\CFEFYHKCDNTCMESVKNGTYDYPKYSEEAKLNREKIDGVKLESTRIYQILAIYSTVASSLVLVVSLGAISFWMCSNGSLQCRIC',\n", + " 'MKAILVVMLYTFTTANADTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCKLRGVAPLHLGQCNIAGWILG\\\n", + "NPECESLSTARSWSYIVETSNSDNGTCYPGDFINYEELREQLSSVSSFERFEIFPKTSSWPNHDSDNGVTAACPHAGAKS\\\n", + "FYKNLIWLVKKGKSYPKINQTYINDKGKEVLVLWGIHHPPTITDQESLYQNADAYVFVGTSRYSKKFKPEIAARPKVRDQ\\\n", + "AGRMNYYWTLVEPGDKITFEATGNLVAPRYAFTMEKDAGSGIIISDTPVHDCNTTCQTPEGAINTSLPFQNVHPITIGKC\\\n", + "PKYVRSTKLRLATGLRNVPSIQSRGLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDKITNKVNSVI\\\n", + "EKMNTQFTAVGKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRNQLKNNAKEIGNG\\\n", + "CFEFYHKCDNTCMESVKNGTYDYPKYSEEAKLNREKIDGVKLDSTRIYQILAIYSTVASSLVLVVSLGAISFWMCSNGSL\\\n", + "QCRIC',\n", + "'MKAVLVVLLYTVTNANADTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLETRHNGKLCKLKGVAPLHLGKCNIAGWLLG\\\n", + "NPECESLSTASSWSYIVETSNSENGTCYPGDFINYEELREQLSSVSSFERFEIFPKTSSWPNHETDKGVTAACPHAGTRS\\\n", + "FYRNLVWLVQKGNSYPKVNTSYINNKGKEVLVLWAIHHPSTSSDQQSLYKNEDAYVFVGSSRYSRKFEPEIATRPKVRDQ\\\n", + "AGRMNYYWTLVEPGDKITFEATGNLVAPRYAFALKRNSGSGIIISDASVHDCDTTCQTPNGAINTSLPFQNIHPVTIGEC\\\n", + "PKYVKSTKLRMATGLRNIPSIQSRGLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADLKSTQSAIDGITNKVNSVI\\\n", + "EKMNTQFTAVGKEFSYLEKRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRSQLKNNAKEIGNG\\\n", + "CFEFYHKCDDMCMESVKNGTYDYPKYSEEAKLNREEIDGVKLESTRIYQILAIYSTVASSLVLVVSLGAISFWMCSNGSL\\\n", + "QCRIC',\n", + "'MKTIIALSNILCLVFAQKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICGSPHQILDGGNC\\\n", + "TLIDALLGDPQCDGFQNKEWDLFVERSRANSNCYPYDVPGYASLRSLVASSGTLEFKNESFNWTGVKQNGTSSACIRGSS\\\n", + "SSFFSRLNWLTSINNIYPAQNVTMPNKEQFDKLYIWGVHHPDTDKNQISLFAQSSGRITVSTKRSQQAVIPNIGSRPRIR\\\n", + "DIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRNGKSSIMRSDAPIGRCKSECITPNGSIPNDKPFQNVNRITYGA\\\n", + "CPRYVKQSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRL\\\n", + "IGKTNEKFHQIEKEFSEVEGRVQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGN\\\n", + "GCFKIYHKCDNACIGSIRNETYDHNVYRDEALNNRFQIKGVELKSGYKDWILWISFAMSCFLLCIALLGFIMWACQKGNI\\\n", + "RCNIC',\n", + "'MKTIIALSNILCLVFAQKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICNSPHQILDGGNC\\\n", + "TLIDALLGDPQCDGFQNKEWDLFVERSRANSSCYPYDVPDYASLRSLVASSGTLEFKNESFNWTGVKQNGTSSACIRGSS\\\n", + "SSFFSRLNWLTSLNNIYPAQNVTMPNKEQFDKLYIWGVHHPDTDKNQFSLFAQSSGRITVSTKRSQQAVIPNIGSRPRIR\\\n", + "DIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRITYGA\\\n", + "CPRYVKQSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQISGKLNRL\\\n", + "IGKTNEKFHQIEKEFSEVEGRVQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGN\\\n", + "GCFKIYHKCDNACIGSIRNETYDHNVYRDEALNNRFQIKGVELKSGYKDWILWISFAMSCFLLCIALLGFIMWACQKGNI\\\n", + "RCNIC',\n", + "'MKTIIALSNILCLVFAQKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILDGGNC\\\n", + "TLIDALLGDPQCDGFQNKEWDLFVERSRANSNCYPYDVPDYASLRSLVASSGTLEFKNESFNWTGVKQNGTSSACIRGSS\\\n", + "SSFFSRLNWLTSLNNIYPAQNVTMPNKEQFDKLYIWGVHHPDTDKNQISLFAQSSGRITVSTKRSQQAVIPNIGSRPRIR\\\n", + "DIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRITYGA\\\n", + "CPRYVKQSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRL\\\n", + "IGKTNEKFHQIEKEFSEVEGRVQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGN\\\n", + "GCFKIYHKCDNACIGSIRNETYDHNVYRDEALNNRFQIKGVELKSGYKDWILWISFAMSCFLLCIALLGFIMWACQKGNI\\\n", + "RCNIC']" + ] + }, + { + "cell_type": "code", + "execution_count": 109, + "id": "33d74ba3", + "metadata": {}, + "outputs": [], + "source": [ + "def getLav(s,seq0):\n", + " from Levenshtein import distance\n", + " return np.array([distance(s,x) for x in seq0]).min()" + ] + }, + { + "cell_type": "code", + "execution_count": 115, + "id": "65b0cf9d", + "metadata": {}, + "outputs": [], + "source": [ + "high_risk_rbd = [getLav(x,seq0) for x in df_.frag_rbd.values]\n", + "df_['hr_rbd'] = high_risk_rbd\n", + "high_risk_rbd = [getLav(x,seq0) for x in df_.frag_sel.values]\n", + "df_['hr_sel'] = high_risk_rbd\n", + "high_risk_rbd = [getLav(x,seq0) for x in df_.frag_pocket.values]\n", + "df_['hr_pocket'] = high_risk_rbd" + ] + }, + { + "cell_type": "code", + "execution_count": 117, + "id": "096ff036", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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emergence_riskimpact_riskmean_geom_riskmean_ha_riskmax_ha_riskmin_ha_riskhr_pocket
edit distance
RBD-0.3790370.0459750.3259850.1697150.1615800.114448NaN
On seleted residues-0.1128980.035949-0.148383-0.461506-0.399043-0.509472NaN
pocketNaNNaNNaNNaNNaNNaNNaN
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" + ], + "text/plain": [ + " emergence_risk impact_risk mean_geom_risk \\\n", + "edit distance \n", + "RBD -0.379037 0.045975 0.325985 \n", + "On seleted residues -0.112898 0.035949 -0.148383 \n", + "pocket NaN NaN NaN \n", + "\n", + " mean_ha_risk max_ha_risk min_ha_risk hr_pocket \n", + "edit distance \n", + "RBD 0.169715 0.161580 0.114448 NaN \n", + "On seleted residues -0.461506 -0.399043 -0.509472 NaN \n", + "pocket NaN NaN NaN NaN " + ] + }, + "execution_count": 117, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "tf=df_[df_.is_irat==1].drop('is_irat',axis=1).corr().loc[['hr_rbd','hr_sel','hr_pocket'],:]\n", + "tf.index=['RBD','On seleted residues',\"pocket\"]\n", + "tf.index.name='edit distance'\n", + "tf.drop(['hr_rbd','hr_sel'],axis=1)" + ] + }, + { + "cell_type": "code", + "execution_count": 112, + "id": "b685a5a6", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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emergence_riskimpact_riskha_riskgeometric_mean_riskfrag_rbdfrag_selmean_geom_riskmean_ha_riskmax_ha_riskmin_ha_riskhr_rbdhr_selfrag_pocket
id
A/swine/Shandong/1207/20167.56.9[0.059268942695459764, 0.059207549599012387, 0...[0.04961693798040306, 0.04939691038300986, 0.0...NSWSYIIETSNSKNGACYPGEFADYEELKEQLSTVSSFERFEIFPK...NSWSYSGANSFLVIWGVSKYYKRF0.0495310.0593250.0598090.059069450541LVIWGVHHPP
A/Ohio/13/20176.65.8[0.007443436845452373, 0.007528108280118501, 0...[0.02257302209884124, 0.0227066090672604, 0.02...QCDGFQNNKWDLFVERSKAHSNCYPYDVPDYASLRSLVASSGTLEF...QCDGFKRRSSNDKLYIWSTKRNQQ0.0237800.0084550.0174830.007363435541DKLYIWGVHH
A/Hong Kong/125/20176.57.5[0.008053012400112526, 0.011702039255706398, 0...[0.0037028892207661, 0.004325280096255358, 0.0...SADLIIERREGSDVCYPGKFVNEEALRQILRESGGIDKETMGFTYN...SADLIAEMKWLIHHSVSSFVPSPG0.0054810.0097870.0124530.005927466542IHHSVSTAEQ
A/Shanghai/02/20136.47.2[0.0029756019607934496, 0.003893470493957003, ...[0.00210888252534967, 0.002386143249933443, 0....SADLIIERREGSDVCYPGKFVNEEALRQILRESGGIDKEAMGFTYS...SADLIAEMKWLIHHSVSSFVPSPG0.0028460.0031310.0038930.002597468542IHHSVSTAEQ
A/Anhui-Lujiang/39/20186.25.9[0.013913606506215747, 0.014682700295856159, 0...[0.018971508708604274, 0.025275351068975476, 0...GREWSYIVERPSAVNGLCYPGNVENLEELRSLFSSARSYQRIQIFP...GREWSYRSMRWNHPPTDFKPLIGP0.0220340.0146390.0176850.012083467542NHPPTDDTQR
A/Indiana/08/20116.04.5[0.015833187603574352, 0.01579698562348106, 0....[0.016902504332314258, 0.01683599355230769, 0....HCDDFQNKEWDLFVERSTAYSNCYPYYVPDYATLRSLVASSGNLEF...HCDDFRRGSVNDKLYIWSTKRSQQ0.0173260.0167890.0256310.015772443541DKLYIWGVHH
A/California/62/20185.85.7[0.25421003694129446, 0.17137241238504203, 0.1...[0.11064301441040252, 0.08010185536798671, 0.0...ESWSYIVETSNPENGTCYPGYFEDYEELREQLSSVSSFKKFEIFPK...ESWSYGNSSFYVLWGVHHYSRRFT0.0940640.1961000.2542100.153140452541VLWGVHHPSN
A/Bangladesh/0994/20115.65.4[0.047962278609110426, 0.047376021553330504, 0...[0.1509708016952567, 0.14755990149418968, 0.15...GREWSYIVERPSAVNGTCYPGNVENLEELRTLFSSSSSYQRIQIFP...GREWSYRNMRWHHPPTDFKPLIGP0.1483340.0471220.0487920.044856468542HHPPTDTAQT
A/Sichuan/06681/20215.36.3[0.3401659563640977, 0.4372884849313668, 0.335...[0.14098323610429828, 0.16479919492131653, 0.1...EWSYIVERANPANDLCYPGSLNDYEELKHLLSRINHFEKILIIPKG...EWSYIAPSFFRLWGIHHLNQRLVP0.1443360.3409750.4372880.293157460541LWGIHHSNNA
A/Vietnam/1203/20045.26.6[0.12775494527491757, 0.11190370497308454, 0.1...[0.07357578392227798, 0.06512340773617227, 0.0...EWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQIIPKS...EWSYIKSSFFRLWGIHHLNQRLVP0.0709490.1287440.1570390.107543465541LWGIHHPNDA
A/Yunnan/14564/20155.06.6[0.20080863109685176, 0.10301992847449411, 0.2...[0.08744456695565636, 0.05634300538887098, 0.0...EWSYIVERANPANDLCYPGNLNDYEELKHLLSRINHFEKTLIIPKS...EWSYIPSFFRNWGIHHSNQRLEPK0.0904330.2062270.2502670.103020462541WGIHHSNNAA
A/Astrakhan/3212/20204.65.2[0.2452941610025089, 0.2335184366024988, 0.221...[0.3660547134708487, 0.352999397804964, 0.3433...EWSYIVERANPANDLCYPGSLNDYEELKHLLSRINHFEKILIIPKS...EWSYIAPSFFRLWGIHHLNQRLVP0.3499130.2267280.2452940.196373460541LWGIHHSNNA
A/Netherlands/219/20034.65.8[0.16431983904493178, 0.16426481855673325, 0.1...[0.2735882731677115, 0.27353672735391277, 0.27...SADLIIERREGSDVCYPGKFVNEEALRQILRESGGIDKETMGFTYS...SADLIAEMKWLIHHSGSSFVPSPG0.2735390.1643360.1645750.163875466542IHHSGSTTEQ
A/American wigeon/South Carolina/AH0195145/20214.45.1[0.22507345650411203, 0.253385372610634, 0.250...[0.2618009640888491, 0.28041946959711944, 0.27...EWSYIVERANPANDLCYPGSLNDYEELKHMLSRINHFEKILIIPKS...EWSYIAPSFFRLWGIHHLNQRLAP0.2665840.2310730.2541590.212808460541LWGIHHSNNA
A/Jiangxi-Donghu/346/20134.36.0[0.03929273071556801, 0.3559593557688923, 0.15...[0.027090727115239115, 0.1774459269887038, 0.0...WDTLIERENAIAYCYPGATVNVEALRQKIMESGGINKISTGFTYGS...WDTLIYAELKWGIHHPSNNFVPVV0.2021980.2097160.3683740.039293468542GIHHPSSTQE
A/gyrfalcon/Washington/41088/20144.24.6[0.24718594726896237, 0.2361702553946631, 0.22...[0.36678073190475535, 0.35436513753260845, 0.3...EWSYIVERANPANDLCYPGTLNDYEELKHLLSRINHFEKTLIIPRS...EWSYIASSFFRLWGIHHLNQRLVP0.3511170.2289410.2471860.198971462541LWGIHHSNNA
A/Northern pintail/Washington/40964/20143.84.1[0.2410948922603147, 0.22971447028474637, 0.21...[0.349366042786461, 0.34039602323151935, 0.331...EWSYIVERANPANDLCYPGTLNDYEELKHLLSRINHFEKNLIIPRS...EWSYIASSFFRLWGIHHLNQRLVP0.3354840.2232690.2410950.195036462541LWGIHHSNNA
A/canine/Illinois/12191/20153.73.7[0.01616230298118454, 0.016067588755834316, 0....[0.024453287740176615, 0.024374121053616235, 0...HCDVFQNETWDLFVERSNAFSNCYPYDVPDYASLRSIVASSGTLEF...HCDVFKRGPANDKLYIWSTRRSQQ0.0250450.0170880.0259810.016030447541DKLYIWGVHH
A/American green-winged teal/Washington/1957050/20143.64.1[0.22532859992890514, 0.2523992705219045, 0.24...[0.2592089036823605, 0.2766319981079351, 0.273...EWSYIVERANPANDLCYPGTLNDYEELKHLLSRINHFEKTLIIPRS...EWSYIASSFFRLWGIHHLNQRLVP0.2633590.2307410.2530980.213461462541LWGIHHSNNA
A/turkey/Indiana/1573-2/20163.43.9[0.042531258378212616, 0.046850178126532895, 0...[0.13246011857462825, 0.13903537495472926, 0.1...DADLIIERREGTDVCYPGKFTNKESLRQILRGSGGIDKESMGFTYS...DADLIAEMKWLVHHSGSSFTPSPG0.1350010.0441940.0468500.041007468542VHHSGSVTEQ
A/chicken/Tennessee/17-007431-3/20173.13.5[0.032175814200484966, 0.03682965073244792, 0....[0.12816247069024164, 0.1371356157354049, 0.12...DADLIIERREGTDVCYPGKFTNEESLRQILRGSGGIDKESMGFTYS...DADLIAEMKWLVHHSGSSFTPSPG0.1314200.0339370.0368300.030574466542VHHSGSADEQ
A/chicken/Tennessee/17-007147-2/20172.83.5[0.082518541655176, 0.08595812903880762, 0.083...[0.20524466180722442, 0.20950526315825033, 0.2...DADLIIERREGTDVCYPGKFTNEESLRQILRGSGGIDKESMGFTYS...DADLIAEMKWLVHHSGSSFTPSPG0.2066110.0838170.0859580.081610468542VHHSGSAAEQ
\n", + "
" + ], + "text/plain": [ + " emergence_risk \\\n", + "id \n", + "A/swine/Shandong/1207/2016 7.5 \n", + "A/Ohio/13/2017 6.6 \n", + "A/Hong Kong/125/2017 6.5 \n", + "A/Shanghai/02/2013 6.4 \n", + "A/Anhui-Lujiang/39/2018 6.2 \n", + "A/Indiana/08/2011 6.0 \n", + "A/California/62/2018 5.8 \n", + "A/Bangladesh/0994/2011 5.6 \n", + "A/Sichuan/06681/2021 5.3 \n", + "A/Vietnam/1203/2004 5.2 \n", + "A/Yunnan/14564/2015 5.0 \n", + "A/Astrakhan/3212/2020 4.6 \n", + "A/Netherlands/219/2003 4.6 \n", + "A/American wigeon/South Carolina/AH0195145/2021 4.4 \n", + "A/Jiangxi-Donghu/346/2013 4.3 \n", + "A/gyrfalcon/Washington/41088/2014 4.2 \n", + "A/Northern pintail/Washington/40964/2014 3.8 \n", + "A/canine/Illinois/12191/2015 3.7 \n", + "A/American green-winged teal/Washington/1957050... 3.6 \n", + "A/turkey/Indiana/1573-2/2016 3.4 \n", + "A/chicken/Tennessee/17-007431-3/2017 3.1 \n", + "A/chicken/Tennessee/17-007147-2/2017 2.8 \n", + "\n", + " impact_risk \\\n", + "id \n", + "A/swine/Shandong/1207/2016 6.9 \n", + "A/Ohio/13/2017 5.8 \n", + "A/Hong Kong/125/2017 7.5 \n", + "A/Shanghai/02/2013 7.2 \n", + "A/Anhui-Lujiang/39/2018 5.9 \n", + "A/Indiana/08/2011 4.5 \n", + "A/California/62/2018 5.7 \n", + "A/Bangladesh/0994/2011 5.4 \n", + "A/Sichuan/06681/2021 6.3 \n", + "A/Vietnam/1203/2004 6.6 \n", + "A/Yunnan/14564/2015 6.6 \n", + "A/Astrakhan/3212/2020 5.2 \n", + "A/Netherlands/219/2003 5.8 \n", + "A/American wigeon/South Carolina/AH0195145/2021 5.1 \n", + "A/Jiangxi-Donghu/346/2013 6.0 \n", + "A/gyrfalcon/Washington/41088/2014 4.6 \n", + "A/Northern pintail/Washington/40964/2014 4.1 \n", + "A/canine/Illinois/12191/2015 3.7 \n", + "A/American green-winged teal/Washington/1957050... 4.1 \n", + "A/turkey/Indiana/1573-2/2016 3.9 \n", + "A/chicken/Tennessee/17-007431-3/2017 3.5 \n", + "A/chicken/Tennessee/17-007147-2/2017 3.5 \n", + "\n", + " ha_risk \\\n", + "id \n", + "A/swine/Shandong/1207/2016 [0.059268942695459764, 0.059207549599012387, 0... \n", + "A/Ohio/13/2017 [0.007443436845452373, 0.007528108280118501, 0... \n", + "A/Hong Kong/125/2017 [0.008053012400112526, 0.011702039255706398, 0... \n", + "A/Shanghai/02/2013 [0.0029756019607934496, 0.003893470493957003, ... \n", + "A/Anhui-Lujiang/39/2018 [0.013913606506215747, 0.014682700295856159, 0... \n", + "A/Indiana/08/2011 [0.015833187603574352, 0.01579698562348106, 0.... \n", + "A/California/62/2018 [0.25421003694129446, 0.17137241238504203, 0.1... \n", + "A/Bangladesh/0994/2011 [0.047962278609110426, 0.047376021553330504, 0... \n", + "A/Sichuan/06681/2021 [0.3401659563640977, 0.4372884849313668, 0.335... \n", + "A/Vietnam/1203/2004 [0.12775494527491757, 0.11190370497308454, 0.1... \n", + "A/Yunnan/14564/2015 [0.20080863109685176, 0.10301992847449411, 0.2... \n", + "A/Astrakhan/3212/2020 [0.2452941610025089, 0.2335184366024988, 0.221... \n", + "A/Netherlands/219/2003 [0.16431983904493178, 0.16426481855673325, 0.1... \n", + "A/American wigeon/South Carolina/AH0195145/2021 [0.22507345650411203, 0.253385372610634, 0.250... \n", + "A/Jiangxi-Donghu/346/2013 [0.03929273071556801, 0.3559593557688923, 0.15... \n", + "A/gyrfalcon/Washington/41088/2014 [0.24718594726896237, 0.2361702553946631, 0.22... \n", + "A/Northern pintail/Washington/40964/2014 [0.2410948922603147, 0.22971447028474637, 0.21... \n", + "A/canine/Illinois/12191/2015 [0.01616230298118454, 0.016067588755834316, 0.... \n", + "A/American green-winged teal/Washington/1957050... [0.22532859992890514, 0.2523992705219045, 0.24... \n", + "A/turkey/Indiana/1573-2/2016 [0.042531258378212616, 0.046850178126532895, 0... \n", + "A/chicken/Tennessee/17-007431-3/2017 [0.032175814200484966, 0.03682965073244792, 0.... \n", + "A/chicken/Tennessee/17-007147-2/2017 [0.082518541655176, 0.08595812903880762, 0.083... \n", + "\n", + " geometric_mean_risk \\\n", + "id \n", + "A/swine/Shandong/1207/2016 [0.04961693798040306, 0.04939691038300986, 0.0... \n", + "A/Ohio/13/2017 [0.02257302209884124, 0.0227066090672604, 0.02... \n", + "A/Hong Kong/125/2017 [0.0037028892207661, 0.004325280096255358, 0.0... \n", + "A/Shanghai/02/2013 [0.00210888252534967, 0.002386143249933443, 0.... \n", + "A/Anhui-Lujiang/39/2018 [0.018971508708604274, 0.025275351068975476, 0... \n", + "A/Indiana/08/2011 [0.016902504332314258, 0.01683599355230769, 0.... \n", + "A/California/62/2018 [0.11064301441040252, 0.08010185536798671, 0.0... \n", + "A/Bangladesh/0994/2011 [0.1509708016952567, 0.14755990149418968, 0.15... \n", + "A/Sichuan/06681/2021 [0.14098323610429828, 0.16479919492131653, 0.1... \n", + "A/Vietnam/1203/2004 [0.07357578392227798, 0.06512340773617227, 0.0... \n", + "A/Yunnan/14564/2015 [0.08744456695565636, 0.05634300538887098, 0.0... \n", + "A/Astrakhan/3212/2020 [0.3660547134708487, 0.352999397804964, 0.3433... \n", + "A/Netherlands/219/2003 [0.2735882731677115, 0.27353672735391277, 0.27... \n", + "A/American wigeon/South Carolina/AH0195145/2021 [0.2618009640888491, 0.28041946959711944, 0.27... \n", + "A/Jiangxi-Donghu/346/2013 [0.027090727115239115, 0.1774459269887038, 0.0... \n", + "A/gyrfalcon/Washington/41088/2014 [0.36678073190475535, 0.35436513753260845, 0.3... \n", + "A/Northern pintail/Washington/40964/2014 [0.349366042786461, 0.34039602323151935, 0.331... \n", + "A/canine/Illinois/12191/2015 [0.024453287740176615, 0.024374121053616235, 0... \n", + "A/American green-winged teal/Washington/1957050... [0.2592089036823605, 0.2766319981079351, 0.273... \n", + "A/turkey/Indiana/1573-2/2016 [0.13246011857462825, 0.13903537495472926, 0.1... \n", + "A/chicken/Tennessee/17-007431-3/2017 [0.12816247069024164, 0.1371356157354049, 0.12... \n", + "A/chicken/Tennessee/17-007147-2/2017 [0.20524466180722442, 0.20950526315825033, 0.2... \n", + "\n", + " frag_rbd \\\n", + "id \n", + "A/swine/Shandong/1207/2016 NSWSYIIETSNSKNGACYPGEFADYEELKEQLSTVSSFERFEIFPK... \n", + "A/Ohio/13/2017 QCDGFQNNKWDLFVERSKAHSNCYPYDVPDYASLRSLVASSGTLEF... \n", + "A/Hong Kong/125/2017 SADLIIERREGSDVCYPGKFVNEEALRQILRESGGIDKETMGFTYN... \n", + "A/Shanghai/02/2013 SADLIIERREGSDVCYPGKFVNEEALRQILRESGGIDKEAMGFTYS... \n", + "A/Anhui-Lujiang/39/2018 GREWSYIVERPSAVNGLCYPGNVENLEELRSLFSSARSYQRIQIFP... \n", + "A/Indiana/08/2011 HCDDFQNKEWDLFVERSTAYSNCYPYYVPDYATLRSLVASSGNLEF... \n", + "A/California/62/2018 ESWSYIVETSNPENGTCYPGYFEDYEELREQLSSVSSFKKFEIFPK... \n", + "A/Bangladesh/0994/2011 GREWSYIVERPSAVNGTCYPGNVENLEELRTLFSSSSSYQRIQIFP... \n", + "A/Sichuan/06681/2021 EWSYIVERANPANDLCYPGSLNDYEELKHLLSRINHFEKILIIPKG... \n", + "A/Vietnam/1203/2004 EWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQIIPKS... \n", + "A/Yunnan/14564/2015 EWSYIVERANPANDLCYPGNLNDYEELKHLLSRINHFEKTLIIPKS... \n", + "A/Astrakhan/3212/2020 EWSYIVERANPANDLCYPGSLNDYEELKHLLSRINHFEKILIIPKS... \n", + "A/Netherlands/219/2003 SADLIIERREGSDVCYPGKFVNEEALRQILRESGGIDKETMGFTYS... \n", + "A/American wigeon/South Carolina/AH0195145/2021 EWSYIVERANPANDLCYPGSLNDYEELKHMLSRINHFEKILIIPKS... \n", + "A/Jiangxi-Donghu/346/2013 WDTLIERENAIAYCYPGATVNVEALRQKIMESGGINKISTGFTYGS... \n", + "A/gyrfalcon/Washington/41088/2014 EWSYIVERANPANDLCYPGTLNDYEELKHLLSRINHFEKTLIIPRS... \n", + "A/Northern pintail/Washington/40964/2014 EWSYIVERANPANDLCYPGTLNDYEELKHLLSRINHFEKNLIIPRS... \n", + "A/canine/Illinois/12191/2015 HCDVFQNETWDLFVERSNAFSNCYPYDVPDYASLRSIVASSGTLEF... \n", + "A/American green-winged teal/Washington/1957050... EWSYIVERANPANDLCYPGTLNDYEELKHLLSRINHFEKTLIIPRS... \n", + "A/turkey/Indiana/1573-2/2016 DADLIIERREGTDVCYPGKFTNKESLRQILRGSGGIDKESMGFTYS... \n", + "A/chicken/Tennessee/17-007431-3/2017 DADLIIERREGTDVCYPGKFTNEESLRQILRGSGGIDKESMGFTYS... \n", + "A/chicken/Tennessee/17-007147-2/2017 DADLIIERREGTDVCYPGKFTNEESLRQILRGSGGIDKESMGFTYS... \n", + "\n", + " frag_sel \\\n", + "id \n", + "A/swine/Shandong/1207/2016 NSWSYSGANSFLVIWGVSKYYKRF \n", + "A/Ohio/13/2017 QCDGFKRRSSNDKLYIWSTKRNQQ \n", + "A/Hong Kong/125/2017 SADLIAEMKWLIHHSVSSFVPSPG \n", + "A/Shanghai/02/2013 SADLIAEMKWLIHHSVSSFVPSPG \n", + "A/Anhui-Lujiang/39/2018 GREWSYRSMRWNHPPTDFKPLIGP \n", + "A/Indiana/08/2011 HCDDFRRGSVNDKLYIWSTKRSQQ \n", + "A/California/62/2018 ESWSYGNSSFYVLWGVHHYSRRFT \n", + "A/Bangladesh/0994/2011 GREWSYRNMRWHHPPTDFKPLIGP \n", + "A/Sichuan/06681/2021 EWSYIAPSFFRLWGIHHLNQRLVP \n", + "A/Vietnam/1203/2004 EWSYIKSSFFRLWGIHHLNQRLVP \n", + "A/Yunnan/14564/2015 EWSYIPSFFRNWGIHHSNQRLEPK \n", + "A/Astrakhan/3212/2020 EWSYIAPSFFRLWGIHHLNQRLVP \n", + "A/Netherlands/219/2003 SADLIAEMKWLIHHSGSSFVPSPG \n", + "A/American wigeon/South Carolina/AH0195145/2021 EWSYIAPSFFRLWGIHHLNQRLAP \n", + "A/Jiangxi-Donghu/346/2013 WDTLIYAELKWGIHHPSNNFVPVV \n", + "A/gyrfalcon/Washington/41088/2014 EWSYIASSFFRLWGIHHLNQRLVP \n", + "A/Northern pintail/Washington/40964/2014 EWSYIASSFFRLWGIHHLNQRLVP \n", + "A/canine/Illinois/12191/2015 HCDVFKRGPANDKLYIWSTRRSQQ \n", + "A/American green-winged teal/Washington/1957050... EWSYIASSFFRLWGIHHLNQRLVP \n", + "A/turkey/Indiana/1573-2/2016 DADLIAEMKWLVHHSGSSFTPSPG \n", + "A/chicken/Tennessee/17-007431-3/2017 DADLIAEMKWLVHHSGSSFTPSPG \n", + "A/chicken/Tennessee/17-007147-2/2017 DADLIAEMKWLVHHSGSSFTPSPG \n", + "\n", + " mean_geom_risk \\\n", + "id \n", + "A/swine/Shandong/1207/2016 0.049531 \n", + "A/Ohio/13/2017 0.023780 \n", + "A/Hong Kong/125/2017 0.005481 \n", + "A/Shanghai/02/2013 0.002846 \n", + "A/Anhui-Lujiang/39/2018 0.022034 \n", + "A/Indiana/08/2011 0.017326 \n", + "A/California/62/2018 0.094064 \n", + "A/Bangladesh/0994/2011 0.148334 \n", + "A/Sichuan/06681/2021 0.144336 \n", + "A/Vietnam/1203/2004 0.070949 \n", + "A/Yunnan/14564/2015 0.090433 \n", + "A/Astrakhan/3212/2020 0.349913 \n", + "A/Netherlands/219/2003 0.273539 \n", + "A/American wigeon/South Carolina/AH0195145/2021 0.266584 \n", + "A/Jiangxi-Donghu/346/2013 0.202198 \n", + "A/gyrfalcon/Washington/41088/2014 0.351117 \n", + "A/Northern pintail/Washington/40964/2014 0.335484 \n", + "A/canine/Illinois/12191/2015 0.025045 \n", + "A/American green-winged teal/Washington/1957050... 0.263359 \n", + "A/turkey/Indiana/1573-2/2016 0.135001 \n", + "A/chicken/Tennessee/17-007431-3/2017 0.131420 \n", + "A/chicken/Tennessee/17-007147-2/2017 0.206611 \n", + "\n", + " mean_ha_risk max_ha_risk \\\n", + "id \n", + "A/swine/Shandong/1207/2016 0.059325 0.059809 \n", + "A/Ohio/13/2017 0.008455 0.017483 \n", + "A/Hong Kong/125/2017 0.009787 0.012453 \n", + "A/Shanghai/02/2013 0.003131 0.003893 \n", + "A/Anhui-Lujiang/39/2018 0.014639 0.017685 \n", + "A/Indiana/08/2011 0.016789 0.025631 \n", + "A/California/62/2018 0.196100 0.254210 \n", + "A/Bangladesh/0994/2011 0.047122 0.048792 \n", + "A/Sichuan/06681/2021 0.340975 0.437288 \n", + "A/Vietnam/1203/2004 0.128744 0.157039 \n", + "A/Yunnan/14564/2015 0.206227 0.250267 \n", + "A/Astrakhan/3212/2020 0.226728 0.245294 \n", + "A/Netherlands/219/2003 0.164336 0.164575 \n", + "A/American wigeon/South Carolina/AH0195145/2021 0.231073 0.254159 \n", + "A/Jiangxi-Donghu/346/2013 0.209716 0.368374 \n", + "A/gyrfalcon/Washington/41088/2014 0.228941 0.247186 \n", + "A/Northern pintail/Washington/40964/2014 0.223269 0.241095 \n", + "A/canine/Illinois/12191/2015 0.017088 0.025981 \n", + "A/American green-winged teal/Washington/1957050... 0.230741 0.253098 \n", + "A/turkey/Indiana/1573-2/2016 0.044194 0.046850 \n", + "A/chicken/Tennessee/17-007431-3/2017 0.033937 0.036830 \n", + "A/chicken/Tennessee/17-007147-2/2017 0.083817 0.085958 \n", + "\n", + " min_ha_risk hr_rbd \\\n", + "id \n", + "A/swine/Shandong/1207/2016 0.059069 450 \n", + "A/Ohio/13/2017 0.007363 435 \n", + "A/Hong Kong/125/2017 0.005927 466 \n", + "A/Shanghai/02/2013 0.002597 468 \n", + "A/Anhui-Lujiang/39/2018 0.012083 467 \n", + "A/Indiana/08/2011 0.015772 443 \n", + "A/California/62/2018 0.153140 452 \n", + "A/Bangladesh/0994/2011 0.044856 468 \n", + "A/Sichuan/06681/2021 0.293157 460 \n", + "A/Vietnam/1203/2004 0.107543 465 \n", + "A/Yunnan/14564/2015 0.103020 462 \n", + "A/Astrakhan/3212/2020 0.196373 460 \n", + "A/Netherlands/219/2003 0.163875 466 \n", + "A/American wigeon/South Carolina/AH0195145/2021 0.212808 460 \n", + "A/Jiangxi-Donghu/346/2013 0.039293 468 \n", + "A/gyrfalcon/Washington/41088/2014 0.198971 462 \n", + "A/Northern pintail/Washington/40964/2014 0.195036 462 \n", + "A/canine/Illinois/12191/2015 0.016030 447 \n", + "A/American green-winged teal/Washington/1957050... 0.213461 462 \n", + "A/turkey/Indiana/1573-2/2016 0.041007 468 \n", + "A/chicken/Tennessee/17-007431-3/2017 0.030574 466 \n", + "A/chicken/Tennessee/17-007147-2/2017 0.081610 468 \n", + "\n", + " hr_sel frag_pocket \n", + "id \n", + "A/swine/Shandong/1207/2016 541 LVIWGVHHPP \n", + "A/Ohio/13/2017 541 DKLYIWGVHH \n", + "A/Hong Kong/125/2017 542 IHHSVSTAEQ \n", + "A/Shanghai/02/2013 542 IHHSVSTAEQ \n", + "A/Anhui-Lujiang/39/2018 542 NHPPTDDTQR \n", + "A/Indiana/08/2011 541 DKLYIWGVHH \n", + "A/California/62/2018 541 VLWGVHHPSN \n", + "A/Bangladesh/0994/2011 542 HHPPTDTAQT \n", + "A/Sichuan/06681/2021 541 LWGIHHSNNA \n", + "A/Vietnam/1203/2004 541 LWGIHHPNDA \n", + "A/Yunnan/14564/2015 541 WGIHHSNNAA \n", + "A/Astrakhan/3212/2020 541 LWGIHHSNNA \n", + "A/Netherlands/219/2003 542 IHHSGSTTEQ \n", + "A/American wigeon/South Carolina/AH0195145/2021 541 LWGIHHSNNA \n", + "A/Jiangxi-Donghu/346/2013 542 GIHHPSSTQE \n", + "A/gyrfalcon/Washington/41088/2014 541 LWGIHHSNNA \n", + "A/Northern pintail/Washington/40964/2014 541 LWGIHHSNNA \n", + "A/canine/Illinois/12191/2015 541 DKLYIWGVHH \n", + "A/American green-winged teal/Washington/1957050... 541 LWGIHHSNNA \n", + "A/turkey/Indiana/1573-2/2016 542 VHHSGSVTEQ \n", + "A/chicken/Tennessee/17-007431-3/2017 542 VHHSGSADEQ \n", + "A/chicken/Tennessee/17-007147-2/2017 542 VHHSGSAAEQ " + ] + }, + "execution_count": 112, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "df_[df_.is_irat==1].drop('is_irat',axis=1)" + ] + }, + { + "cell_type": "code", + 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emergence_riskimpact_riskmean_geom_riskmean_ha_riskmax_ha_riskmin_ha_risk
hr_rbd-0.781912-0.7915620.6802070.6213450.6259800.616085
hr_sel0.0480720.028948-0.129186-0.244412-0.240427-0.252039
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" + ], + "text/plain": [ + " emergence_risk impact_risk mean_geom_risk mean_ha_risk \\\n", + "hr_rbd -0.781912 -0.791562 0.680207 0.621345 \n", + "hr_sel 0.048072 0.028948 -0.129186 -0.244412 \n", + "\n", + " max_ha_risk min_ha_risk \n", + "hr_rbd 0.625980 0.616085 \n", + "hr_sel -0.240427 -0.252039 " + ] + }, + "execution_count": 113, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "df_.drop('is_irat',axis=1).corr().loc[['hr_rbd','hr_sel'],:].drop(['hr_rbd','hr_sel'],axis=1)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "81387c94", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "a805cdf6", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.7.5" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +}