33:null 34:["$","title",null,{"children":"Evolutionary annotation of global SARS-CoV-2/COVID-19 genomes enabled by data from | Hannah Kim | Observable"}] 3a:T8eb,parseFilterString = (str) => { let locations = {}; // convert ranges, if present into lists let coordinates = {}; _.each (str.split (","), (term)=> { let range = term.split ("-"); if (range.length == 2) { let t1 = parseInt (range[0].replace (' ', '')); if (t1 >= 1 && t1 <= 30000) { let t2 = parseInt (range[1].replace (' ', '')); if (t2>=t1 && t2 <= 30000) { _.each (_.range (t1,t2+1,3), (d)=>coordinates[d] = 1); } } else { let gene_range = _.map (range, (d)=> { let d2 = d.split ("/"); if (d2.length == 2) { return d2; } return [null,null]; }); if (gene_range[0][0] && gene_range[0][0] == gene_range[1][0]) { let t1 = parseInt (gene_range[0][1].replace (' ', '')); if (t1 >= 1 && t1 <= 4000) { let t2 = parseInt (gene_range[1][1].replace (' ', '')); if (t2>=t1 && t2 <= 4000) { _.each (_.range (t1,t2+1,1), (d)=>coordinates[gene_range[0][0].toUpperCase() + "/" + d] = 1); } } } } } else { if (range.length == 1) { coordinates [term.replace (' ', '')] = 1; } } }); _.each (coordinates, (dummy, site)=> { let is = parseInt (site.replace (' ', '')); let s = +is; //let s = 265+Math.floor ((+is-266)/3) * 3; // Because annotationJSON accepts zero-index keys, the coordinate input 21736 in 1-indexing would return the output for 21737 instead. To fix this, s-1 to convert 1-index input to zero-index. if (s-1 in annotationJSON) { locations[s-1] = 1; return; } if (s-2 in annotationJSON) { locations[s-2] = 1; return; } if (s-3 in annotationJSON) { locations[s-3] = 1; return; } site = site.toUpperCase(); if (site in jsonCodonLookup) { locations[jsonCodonLookup[site]] = 1; } }); return _.sortBy (_.map (locations, (d,k)=>+k)); }3b:[] 38:{"id":"58dcf3da003a023a","slug":"evolutionary-annotation-of-global-sars-cov-2-covid-19-genomes","title":"Evolutionary annotation of global SARS-CoV-2/COVID-19 genomes enabled by data from ","thumbnail":"040cd5dc4224d451df89d520998a65c29ecffc7a39e9fae2947e790e02bffaf7","access_level":"public","create_time":"$D2021-06-17T17:54:24.941Z","update_time":"$D2021-06-26T12:00:19.895Z","view_time":null,"first_public_time":"$D2021-06-17T20:01:36.775Z","has_unpublished_edits":null,"fork":{"id":"bbcdd9adf10bc97b","slug":"sars_cov_2_sites","title":"Evolutionary annotation of B.1.1.7 SARS-CoV-2/COVID-19 genomes enabled by data from ","owner":{"id":"9bf992815a7b66f2","login":"spond","name":"Sergei Pond"}},"stars":0,"starred":false,"owner":{"type":"team","id":"da6de0bfa6ca61d7","login":"hannahkimincompbio","name":"Hannah Kim","avatar_url":"https://avatars-next.observableusercontent.com/2df327126449c2f5daa5ad7a5bd24c23eb14bc15f28e94db740cb3f5e47b3134","tier":"starter_2024","bio":"Doctoral Student in Bioinformatics | Temple University"},"version":618,"publish_version":618,"role":null,"authored":false,"authors":[{"type":"individual","id":"fce54e128292c37d","login":"hannahkimincompbio","name":"Hannah Kim","avatar_url":"https://avatars-next.observableusercontent.com/2df327126449c2f5daa5ad7a5bd24c23eb14bc15f28e94db740cb3f5e47b3134","tier":null,"bio":"Doctoral Student in Bioinformatics | Temple University"}],"members":[{"type":"individual","id":"fce54e128292c37d","login":"hannahkimincompbio","name":"Hannah Kim","avatar_url":"https://avatars-next.observableusercontent.com/2df327126449c2f5daa5ad7a5bd24c23eb14bc15f28e94db740cb3f5e47b3134","tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":true,"trashed":false,"lapsed":null,"subscribed":null,"forks":0,"collection":{"id":"cc52446a0f8c687c","slug":"tools-for-sars-cov-2","title":"Tools for SARS-CoV-2","owner":{"id":"da6de0bfa6ca61d7","login":"hannahkimincompbio","name":"Hannah Kim"}},"type":"notebook","body":{"titling":"auto","title":"Evolutionary annotation of global SARS-CoV-2/COVID-19 genomes enabled by data from ","cells":[{"id":0,"value":"md`# Evolutionary annotation of ${title} SARS-CoV-2/COVID-19 genomes enabled by data from $\"gisaid-logo\"$
\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":37,"value":"md`There are **${_.size(annotationJSON)}** codons in the SARS-CoV-2 genome with available annotation evolutionary attributes and **${filteredListOfSites.length}** sites selected for display.`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":336,"value":"viewof selection = text({placeholder : \"413,S/484,RdRp/320-RdRp/325\", submit: \"Lookup\", description: \"Display information about these sites, separate by commas, use nucleotide or Gene/Codon coordinates. Not sure which coordinates to search? See Genbank SARS-CoV-2 reference, Wuhan-Hu-1 (https://www.ncbi.nlm.nih.gov/nuccore/1798174254).\", \"title\" : \"Sites to view\", \"value\" : sitelist})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":95,"value":"md`**Select columns to display**`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":93,"value":"viewof c2d = checkbox({\n \n options: [\n { value: \"n\", label: \"Coordinate\" },\n { value: \"aka\", label: \"AKA\"},\n { value: \"segment\", label: \"Gene\" },\n { value: \"SS\", label: \"Site\" },\n { value: \"MEME.p\", label: \"MEME\" },\n { value: \"MEME.br\", label: \"Events\" },\n { value: \"FEL.p\", label: \"FEL\" },\n { value: \"FEL.kind\", label: \"Type\" },\n { value: \"trend\", label: \"TrendZ\" },\n { value: \"hla\", label: \"Epitopes\" }, \n { value: \"maf\", label: \"MAF\"},\n { value: \"unusual\", label: \"Unexpected\"},\n { value: \"aa\", label: \"Composition\"}\n ],\n value: [\"n\", \"aka\",\"MEME.p\",\"MEME.br\",\"FEL.p\",\"FEL.kind\", \"trend\",\"hla\"],\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":107,"value":"table(rowsForTable, \n {enableFilter : true, enableDownload : true, limit : 500, enableFilter : true\n }\n )","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":447,"value":"siteTableCaption","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":14,"value":"md`--- \n### Code and data below this point`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":31,"value":"md`#### Data`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":98,"value":"rowsForTable = generateSiteRowList (filteredListOfSites, c2d, 0.05)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":77,"value":"filteredListOfSites = {\n return _.map (parseFilterString (selection), (d)=>annotationJSON [d]);\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":571,"value":"$3a","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":345,"value":"jsonCodonLookup = {\n let codons = {};\n _.each (annotationJSON, (d,k)=> {\n if (d.G) {\n codons[d.G.toUpperCase() + \"/\" + d.S] = k;\n codons[d.segment.toUpperCase() + \"/\" + d.SS] = k;\n if (d.G.toUpperCase().substr (0,4) == \"ORF1\") {\n codons[\"ORF1AB/\" + (Math.floor ((k-265)/3) + 1)] = k;\n }\n }\n });\n return codons;\n} ","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":485,"value":"title = new URLSearchParams(location.search).get (\"title\") || \"global\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":17,"value":"md`#### Module Requires`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":22,"value":"d3 = require (\"d3\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":64,"value":"_ = require (\"lodash\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":330,"value":"sitelist = params.get(\"sites\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":332,"value":"params = new URLSearchParams(location.search)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":25,"value":"md`#### Imports`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":28,"value":"import {select,checkbox, autoSelect, text} from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":43,"value":"import {translation_table,translate_ambiguous_codon} from \"@spond/usual-vs-unusual-mutation-analyses\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":315,"value":"import {columns2Display, generateSiteRowList, siteTableCaption,annotationJSON} from \"@spond/evolutionary-annotation-of-sars-cov-2-covid-19-genomes-enab\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":46,"value":"import { table } from \"@gampleman/table\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":51,"value":"import {offsetsByGene} from \"@spond/revised-sars-cov-2-analytics-page\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W3b","stdlib":"1"}} 39:"$38:body"