2c:null 2d:["$","title",null,{"children":"Annotation of SARS-2 Coronavirus Genome | Delphine Lariviere | Observable"}] 32:Tda4,formattedtable= { let newtable=[] for (let row = 0; row < coordtable.length-1; row++) { let refcol = coordtable[row]['Reference']; let references = refcol.split(';'); let regexpnb = /\[[0-9]+\]/; let regexpref =/$(.*?)$/; let x = references.length ; let formatref='' let listref=[]; if(x>1){ let REFLINKS=[]; for (let i = 0; i < x-1; i++) { let nbref=references[i].match(regexpnb); let ref=regexpref.exec(references[i]); if(ref !=null){ listref.push( { num: nbref[0] , doi: ref[1] }); REFLINKS.push(""+ nbref +" "); } else{listref.push({num:"", doi:""}); REFLINKS.push("");}; }; formatref= `${REFLINKS.join(' ')}`; } else{formatref=coordtable[row]['Reference']}; let formatannot='' let annotcol = coordtable[row]['Annotation']; let annotations = annotcol.split(';'); let regexanot=/(.*?)\[[0-9]+?\]/; let y = annotations.length ; if(y>1){ let reftags = []; for (let k = 0; k < y-1; k++) { let nbref=annotations[k].match(regexpnb); let numrefchan=annotations[k].match(regexpnb); if(numrefchan !=null){ let text=regexanot.exec(annotations[k]); let ref=listref.filter(d => d['num'] == numrefchan);//['doi']; if(ref.length>0){ reftags.push(text[1] + " "+ numrefchan +" "); } else { reftags.push(text[1] +" "+numrefchan)} ; } else {reftags.push(annotations[k]);}; }; formatannot= `${reftags.join(';')}`; } else{formatannot=coordtable[row]['Annotation']}; let formatimpact='' let impactcol = coordtable[row]['Impact']; let impacts = impactcol.split(';'); let regeximpact=/(.*?)\[[0-9]+?\]/; let z = impacts.length ; if(z>1){ let impacttags = []; for (let l = 0; l < z-1; l++) { let nbimp=impacts[l].match(regeximpact); let numrefimp=impacts[l].match(regexpnb); if(numrefimp !=null){ let text=regeximpact.exec(impacts[l]); let ref=listref.filter(d => d['num'] == numrefimp);//['doi']; if(ref.length>0){ impacttags.push(text[1] + " "+ numrefimp +" "); } else { impacttags.push(text[1] +" "+numrefimp)} ; } else {impacttags.push(impacts[l]);}; }; formatimpact= `${impacttags.join(';')}`; } else{formatimpact=coordtable[row]['Impact']}; let formatresidue= [] if(coordtable[row]['Variant']=='yes'){ formatresidue= "

" + coordtable[row]['Variant'] + "

" } else{formatresidue= coordtable[row]['Variant']}; newtable.push({NC_045512:coordtable[row]['NC_045512'] , AA:coordtable[row]['AA'] , Genome:coordtable[row]['Genome'] , Variant:formatresidue ,Annotation:formatannot , Impact:formatimpact, Reference:formatref}) }; return newtable; }33:[] 30:{"id":"394e0665ad491fdf","slug":"annotation-of-sars-2-coronavirus-genome","title":"Annotation of SARS-2 Coronavirus Genome","thumbnail":"45c8e60ec423fab5de1365d65fcd9d91e29de436018504d9b955e5c53d15fda4","access_level":"public","create_time":"$D2020-06-05T14:14:01.286Z","update_time":"$D2021-03-26T14:10:00.626Z","view_time":null,"first_public_time":"$D2020-06-16T14:50:07.697Z","has_unpublished_edits":null,"fork":false,"stars":1,"starred":false,"owner":{"type":"team","id":"c5273f08e985ed20","login":"delphine-l","name":"Delphine Lariviere","avatar_url":"https://avatars-next.observableusercontent.com/ae3fa924310c52122255eb2926f4caa5d86db59b42e1ed8700b8e77904ab9e3e","tier":"starter_2024"},"version":692,"publish_version":692,"role":null,"authored":false,"authors":[{"type":"individual","id":"1756539ffd3ac8e7","login":"delphine-l","name":"Delphine Lariviere","avatar_url":"https://avatars-next.observableusercontent.com/ae3fa924310c52122255eb2926f4caa5d86db59b42e1ed8700b8e77904ab9e3e","tier":null}],"members":[{"type":"individual","id":"1756539ffd3ac8e7","login":"delphine-l","name":"Delphine Lariviere","avatar_url":"https://avatars-next.observableusercontent.com/ae3fa924310c52122255eb2926f4caa5d86db59b42e1ed8700b8e77904ab9e3e","tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":1,"collection":null,"type":"notebook","body":{"titling":"auto","title":"Annotation of SARS-2 Coronavirus Genome","cells":[{"id":0,"value":"md`# Annotation of SARS-2 Coronavirus Genome`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":36,"value":"viewof use_gene = {\n const dd3 = select({\n title: \"View annotations of\",\n options:\n list_genes[0]\n });\n dd3.input.style.fontSize = \"30px\";\n dd3.input.style.marginTop = \"8px\";\n dd3.index = list_genes[0].indexOf(dd3.value)\n return dd3\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":690,"value":"viewof range = rangeSlider({\n min: 1,\n max: coordtable.length-1,\n value: [1, coordtable.length-1],\n precision: 0, // how many decimal places\n title: 'Start and end amino-acid positions',\n\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":689,"value":"viewof variants_only = checkbox({\n //description: \"Just a single checkbox to toggle\",\n options: [{ value: \"toggle\", label: \"Show only variants with annotation\" }],\n value: \"toggle\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":86,"value":"summary = table( \n filter_table (),\n {\n limit: 2000,\n enableCSVDownload: true,\n sort: true,\n enableFilter: true,\n columns: [ {\n key: 'NC_045512',\n name:'Position in SARS-CoV-2 gene',\n }, \n {\n key: 'AA',\n name:'Residue',\n },\n {\n key: 'Genome',\n name:'Position in Genome (bp)',\n },\n {\n key: 'Annotation',\n },\n {\n key: 'Impact',\n },\n /*{\n key: 'Variant',\n },*/\n //{\n // key: 'Reference' ,\n //},\n ]} ) ","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":664,"value":"md` To access a searchable and downloadable version of this table, use the [original notebook](https://observablehq.com/@delphine-l/annotation-of-sars-2-coronavirus-genome).`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":673,"value":"md`## How to use the annotation query tool\n\nAnnotations are available for each residue of SARS-CoV-2 genes. \n\n- **Position in SARS-CoV-2 gene** : (1-based) position of the residue in the gene/region of interest\n- **Residue** : the [reference genome](https://www.ncbi.nlm.nih.gov/nuccore/NC_045512.2) residue at this position\n- **Position in Genome (bp)** : the (1-based) nucleotide position of in the reference genome\n- **Annotation** : information about this residue found in literature\n- **Impact** : information about the impact of changes at this residue found in literature\n\n\nSelect the gene and region of interest to display the annotations available in that region. \n- The display is limited to 2000 lines. \n- You can search terms in the table by using the magnifier icon at the bottom left of the table. \n- You can also download the table by using the arrow icon on the bottom right of the table\n- You can sort of columns by clicking on respective headings\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":4,"value":"md`\n## Data and Librairies\n\n### Libraries` ","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":10,"value":"data = require('vega-datasets') // import vega_datasets\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":12,"value":"d3 = require(\"d3@5\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":14,"value":"import { table } from \"@gampleman/table\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":16,"value":"_ = require('lodash')\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":19,"value":"vegalite = require(\"vega-embed@6\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":22,"value":"import {select, checkbox} from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":286,"value":"import {rangeSlider} from '@mootari/range-slider'","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":26,"value":"md` ### Data`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":342,"value":"$32","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":45,"value":"tables_URL = _.sortBy (await d3.tsv(\"https://raw.githubusercontent.com/galaxyproject/SARS-CoV-2/master/genomics/no-more-business-as-usual/7-VariantsDescription/residue_annotation/accessurl.tsv\"), c=>c.gene)\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":32,"value":"list_genes = _.map (['gene', 'url'], (c)=>_.map (tables_URL, (d)=>d[c]))\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":34,"value":"coordtable = await d3.tsv(list_genes[1][ list_genes[0].indexOf(use_gene)]) \n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":682,"value":"filter_table = () => {\n let show_me = formattedtable.filter(d => (+d['NC_045512']) >= range[0] && (+d['NC_045512']) <= range[1] && (!variants_only || d['Annotation'].length || d['Impact'].length));\n if (show_me.length == 0) {\n return [{'NC_045512' : 'No annotated positions'}];\n }\n return show_me;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W33","stdlib":"1"}} 31:"$30:body"