31:Tb24,mutation_classification = { let ms = []; const most_recent = analysis_dates[analysis_dates.length - 1]; _.each (combined_data, (d, coord)=> { let recent_s = _.find (d.S, (dd)=>dd[1] == most_recent); const sel_profile = _.countBy (d.S, (dd)=>dd[4] > dd[3] ? 'P' : 'N'); let site_info = { 'Coord' : coord, 'Gene/site' : [d.L, coord], 'Recent' : recent_s ? (recent_s [4] > recent_s [3] ? '+' : '-') : null, 'Periods' : d.S ? d.S.length : 0, 'Type' : _.size (sel_profile) ? (_.size (sel_profile) == 2 ? 'Alternating' : ('P' in sel_profile ? 'Positive' : 'Negative')) : null, }; _.each (d.V, (var_data)=> { if (var_data[1] != '?' && var_data[1] != '-') { if (var_data[0] != d.C) { let si = _.clone (site_info); si.Freq = var_data[3]; si.Codon = d.C + "→" + var_data[0]; si.AA = [translation_table[d.C] + "→" +var_data[1], d.L.split ('/')[0] + ":" + translation_table[d.C] + d.L.split ('/')[1] + var_data[1]]; if (d.P) { si.Predicted = [d.P [var_data[0]] || 0, d.L]; } else { si.Predicted = [0, d.L]; } if (d.H) { const haplo = _.find (d.H, (h)=>h[0] == var_data[0]); if (haplo) { si.HRank = haplo[2]; } else { si.HRank = 1; } } let adaptive_score = 0; if (si.Recent == '+') adaptive_score += 1; if (si['Type'] == 'Alternating') adaptive_score += 1; adaptive_score += si['Periods'] / analysis_dates.length; if (si.Predicted[0] < 1e-6) { adaptive_score += 1; } adaptive_score += Math.pow (1-si.HRank, 10.); //adaptive_score += 0.5*Math.pow (si.Freq, 1/3); si.AScore = adaptive_score; let conserved_score = 0; if (si.Recent == '-') conserved_score += 1; if (si['Type'] == 'Alternating') conserved_score -= 0.5; conserved_score += si['Periods'] / analysis_dates.length; if (si.Predicted[0] > 1e-4) { conserved_score += 1; } conserved_score += Math.pow (1-si.HRank, 10.); si.CScore = conserved_score; ms.push (si); } } }); }); return ms; }32:Tc29,html` `33:[{"id":"e28bf6c41c2ce5011db7438a82d5d2e644001c5ebee598e5d239b07044f16b9902e6009272bcc2534b7c31894b8129e501afac83d73d02e76b4148cdf25390a4","href":"https://static.observableusercontent.com/files/e28bf6c41c2ce5011db7438a82d5d2e644001c5ebee598e5d239b07044f16b9902e6009272bcc2534b7c31894b8129e501afac83d73d02e76b4148cdf25390a4","name":"combined@1.json","type":"application/json","lastModified":1634500185841.712,"size":8254949}] 2f:{"title":"Evolutionary prioritization of codons and mutations in SARS-CoV-2 genomes enabled by data from ","cells":[{"id":0,"value":"md`# Evolutionary prioritization of codons and mutations in SARS-CoV-2 genomes enabled by data from $\"gisaid-logo\"$
`","pinned":false,"hidden":false,"mode":"ojs"},{"id":2284,"value":"genome_view = vegalite(genome_view_spec (genome_display (pdata, ndata)))","pinned":false,"hidden":false,"mode":"ojs"},{"id":1877,"value":"table1_label = md`**Table 1.** Sites and specific mutations in SARS-CoV-2 prioritized by the Adaptive Score (higher -- more evolutionary interest)\n

About the Adaptive Score

\n To be written\n

\n\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":2172,"value":"viewof table1 = Inputs.table (pdata, {\n rows : 15,\n format: {\n 'Freq' : (x)=>x.toFixed (4),\n 'AA' : (x)=>html`${x[0]}`,\n 'Gene/site' : (x)=>html`${x[0]}`,\n 'Predicted' : (x)=>x[0]\n }\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":2251,"value":"table2_label = md`**Table 2.** Sites and specific mutations in SARS-CoV-2 prioritized by the Conservation Score (higher -- more evolutionary constraint)\n

About the Conservation Score

\n To be written\n

\n\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":2247,"value":"viewof table2 = Inputs.table (ndata, {\n rows : 15,\n format: {\n 'Freq' : (x)=>x.toFixed (4),\n 'AA' : (x)=>html`${x[0]}`,\n 'Gene/site' : (x)=>html`${x[0]}`,\n 'Predicted' : (x)=>x[0]\n }\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":5,"value":"md`### Libraries and data`","pinned":false,"hidden":false,"mode":"ojs"},{"id":9,"value":"d3 = require(\"d3@6\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":1194,"value":"import {select} from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":12,"value":"vegalite = require (\"vega-embed\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":15,"value":"_ = require (\"lodash\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":2113,"value":"analysis_dates = _.sortBy (_.uniqBy (_.flatten(_.map (combined_data, (d)=>_.map (d.S, (dd)=>dd[1])))))","pinned":false,"hidden":false,"mode":"ojs"},{"id":2275,"value":"pdata = _.map (_.sortBy (_.filter (mutation_classification, (d)=>d.AScore >= 4), (d)=>-d.AScore), (d)=>_.pick (d, ['Coord','Gene/site','Recent','Type','Periods','Freq','Codon','AA','Predicted','HRank','AScore']))","pinned":false,"hidden":false,"mode":"ojs"},{"id":2272,"value":"ndata = _.map (_.sortBy (_.filter (mutation_classification, (d)=>d.CScore >= 3.75), (d)=>-d.CScore), (d)=>_.pick (d, ['Coord','Gene/site','Recent','Type','Periods',\n 'Freq','Codon','AA','Predicted','HRank','CScore']))","pinned":false,"hidden":false,"mode":"ojs"},{"id":2127,"value":"$31","pinned":false,"hidden":false,"mode":"ojs"},{"id":2107,"value":"combined_data = await (FileAttachment(\"combined@1.json\").json())","pinned":false,"hidden":false,"mode":"ojs"},{"id":2124,"value":"import {translation_table} from \"@spond/usual-vs-unusual-mutation-analyses\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":2264,"value":"import {genome_view_spec} from \"@spond/selection-profile\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":2268,"value":"genome_display = (pset, nset)=> {\n let site_info = [];\n _.each ([[pset,'Pos'],[nset,'Neg']], (d,i)=> {\n _.each (d[0], (s)=> {\n site_info.push ({\n 'coord' : s.Coord,\n 'label' : s[\"Gene/site\"][0],\n 'Score' : s[i?\"CScore\":\"AScore\"],\n 'type' : d[1]\n });\n });\n });\n return site_info; \n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":1402,"value":"pad_array = (arr)=>_.map (arr, (d)=>\"Site \" + d.toUpperCase())","pinned":false,"hidden":false,"mode":"ojs"},{"id":2280,"value":"genome_display (pdata, ndata)","pinned":false,"hidden":false,"mode":"ojs"},{"id":1630,"value":"$32","pinned":false,"hidden":false,"mode":"ojs"},{"id":1633,"value":"html``","pinned":false,"hidden":false,"mode":"ojs"}],"files":"$W33","stdlib":"1","titling":"auto"}