41:null 42:["$","title",null,{"children":"HyPhy-biowasm | Sergei Pond | Observable"}] 48:Td4d,html` `49:[] 46:{"id":"656424b55f573b98","slug":"hyphy-biowasm","title":"HyPhy-biowasm","thumbnail":"d08bcc278687599b0d043cfb02a6594d1f243c56d103e0d8ab5714655bccf887","access_level":"unlisted","create_time":"$D2023-10-29T16:01:40.166Z","update_time":"$D2025-06-22T23:11:14.150Z","view_time":null,"first_public_time":null,"has_unpublished_edits":null,"fork":{"id":"24395d8ce4957b3b","slug":"hello-biowasm","title":"Hello biowasm","owner":{"id":"3e2c8f51767b407c","login":"josesho","name":"Joses W. Ho"}},"stars":0,"starred":false,"owner":{"type":"team","id":"9bf992815a7b66f2","login":"spond","name":"Sergei Pond","avatar_url":"https://avatars-next.observableusercontent.com/23c8c466a3ef27f1444c95a9ed8e52bcf08888403b6d4efbd039319b0761c13d","tier":"starter_2024","bio":"","following":false},"version":605,"publish_version":null,"role":null,"authored":false,"authors":[{"type":"individual","id":"f439ea11e6786e12","login":"spond","name":"Sergei Pond","avatar_url":"https://avatars-next.observableusercontent.com/23c8c466a3ef27f1444c95a9ed8e52bcf08888403b6d4efbd039319b0761c13d","tier":null,"bio":"","following":false}],"members":[{"type":"individual","id":"f439ea11e6786e12","login":"spond","name":"Sergei Pond","avatar_url":"https://avatars-next.observableusercontent.com/23c8c466a3ef27f1444c95a9ed8e52bcf08888403b6d4efbd039319b0761c13d","tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":1,"collection":null,"type":"notebook","body":{"titling":"auto","title":"HyPhy-biowasm","cells":[{"id":0,"value":"# HyPhy-biowasm","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":131,"value":"## `version`\n Please wait for the version to appear; this will indicate that the .wasm files have loaded","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":146,"value":"{\n let loader = html`

Loading HyPhy...

`;\n loader.value = null;\n yield loader;\n \n yield htl.html`

${hyphy_out.stdout}

`;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":587,"value":"viewof analysis = Inputs.select([\"FEL\", \"MEME\", \"aBSREL\"], {\n label: \"Analysis type\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":210,"value":"## `Run ${analysis} on User Data`","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":215,"value":"viewof file = Inputs.file({label : \"Alignment + tree\"})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":444,"value":"_.isNumber(progress_value)\n ? html`Analysis progress. More details displayed as text below. (${(\n progress_value * 100\n ).toFixed(2)}%)

`\n : html`The analysis is finished.
View ${analysis} results`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":261,"value":"md`${(analysis_update) || \"Waiting for the analysis to start\"}`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":583,"value":"

","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":425,"value":"## Code","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":310,"value":"function update_hyphy_progress(payload) {\n if (payload.type == 'print') {\n if (_.isString (mutable analysis_update)) {\n mutable analysis_update += payload.text;\n }\n } else {\n var pr = payload.text.match (/([0-9]+)\\/([0-9]+)/);\n if (pr) { \n mutable progress_value = parseFloat (pr[1])/parseFloat (pr[2]);\n } else {\n mutable progress_value = 0;\n }\n }\n \n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":213,"value":"input_files = cliObj.cli.mount([\n { name: \"user.nex\", data: await file.blob() }\n])","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":167,"value":"hyphy_fel = {\n mutable analysis_update = \"\";\n let rvi = await cliObj.cli.exec(\n \"hyphy LIBPATH=/shared/hyphy/ \" +\n analysis +\n \" --alignment \" +\n input_files[0] +\n \" --output \" +\n input_files[0] +\n \".json\"\n );\n mutable progress_value = cliObj.cli.download(input_files[0] + \".json\");\n return rvi;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":599,"value":"\"hyphy LIBPATH=/shared/hyphy/ \" +\n analysis +\n \" --alignment \" +\n input_files[0] +\n \" --output \" +\n input_files[0] +\n \".json\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":464,"value":"mutable progress_value = 0.0","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":345,"value":"mutable analysis_update = null","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":99,"value":"hyphy_out = cliObj.cli.exec(\n \"hyphy --version\"\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":121,"value":"## Imports","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":5,"value":"cliObj = ({\n cli: await new Aioli({\n\t\ttool: \"hyphy\",\n\t\tversion: \"2.5.63\",\n\t\t// URL at which .js/.wasm assets are located\n\t urlPrefix: \"https://data.hyphy.org/web/biowasm\"\n\t}, {\n printInterleaved: false,\n callback: (e)=>update_hyphy_progress (e),\n })\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":70,"value":"Aioli = require(\"@biowasm/aioli@3.1.0/dist/aioli.js\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":437,"value":"$48","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W49","stdlib":"1"}} 47:"$46:body"