2f:T95f,{ let fasta = await d3.text("https://raw.githubusercontent.com/aglucaci/AOC-REM2/main/results/mammalian_REM2/mammalian_REM2_codons.SA.FilterOutliers.fasta"); console.log("# Step (1) Starting to define the alignment viewer"); fasta = _.map (fasta.split ('\n'), (l)=>{ if (l[0]=='>') { console.log("# Step (2) Parsing ID:" + l); let p = l.substr(1).split ('_'); console.log("# Step (3) Variable p: " + p); //let a = l.substr(1).split("_"); //console.log("# Step (4) Variable a: " + a); //console.log("# Variable a[0]: " + a[0]); //let f = l.substr(1).split("-"); //console.log("# Step (5) Variable f: " + f); //if (a.length >= 3 || a[0] == "epi" || f[0] == "hCoV" ) { if (p[0] == "hCoV" ) { //let elements = [p[2], f[4]] //if (a[4] == "South" || a[4] == "North") { // console.log ("# Found a South/North"); // //elements = [a[0], a[1], a[2], a[4] + " " + a[5]]; // elements = [a[2], a[4] + " " + a[5]]; //} //let id = ">QUERY|" + elements.join("|"); //console.log ("# QUERY ID: " + id); //return "QUERY"; //return id; return ">" + p //return query_id; } else { //p = l.substr (1).split ('_'); //p = p.splice (3); //p.splice (-2,2); //return '>REF|' + p.join("/"); //let ref_id = '>REF|' + p.join("_"); let elements = [p[0], p[1]] let ref_id = '>' + elements.join("_"); //let ref_id = p.join("_"); console.log("# Step (X) Final alignment ID (REFs): " + ref_id); return ref_id; //return "REF"; } //console.log("Final alignment ID: " + l); return l; } //accumulator += l.replace (" ", ""); if (l.length) { return _.map (_.range (0,l.length,3), (s)=>translate_ambiguous_codon_gap (l.substr (s,3))).join (""); } return ""; }).join ("\n"); ReactDOM.render( React.createElement( a.default, {fasta: a.fastaParser(fasta), site_color:a.colors.amino_acid_color, text_color:a.colors. amino_acid_text_color, centerOnSite: 1 }, null ), document.getElementById('alignment')); }30:T7ce,{ let dim = treeDim.length ? _.map (treeDim.split ("x"), (d)=>+d) : null; console.log("DIM:" + dim); let tree = tree_object[0]; var t = tree.render("#tree_container_0", dim ? { height:dim[0] || 400, width:dim[1] || 600, 'show-scale' : true, 'is-radial' : false, 'left-right-spacing': 'fit-to-size', 'top-bottom-spacing': 'fit-to-size', 'node_circle_size' : (n)=>0 } : { height:400, width:600, 'show-scale' : true, //'left-right-spacing': 'fit-to-size', //'top-bottom-spacing': 'fit-to-size', 'is-radial' : false, 'node_circle_size' : (n)=>0 }); const bs = (n) => { if (tree.is_leafnode (n)) { return 3; } return 1; }; let c10 = d3.scaleOrdinal(d3.schemeDark2); //var c10 = d3.scaleOrdinal(d3.schemeDark2); t.node_label = n=>n.data.name.substr (0,3); t.node_bubble_size = bs; console.log("Bubble size: " + bs); t.phylotree.node_bubble_size = bs; //t.options["draw-size-bubbles"] = nodeStates ? true : false; //t.font_size = 8; //t.spacing_x (7); function sort_nodes (asc) { tree.traverse_and_compute (function (n) { var d = 1; if (n.children && n.children.length) { d += d3.max (n.children, function (d) { return d["count_depth"];}); } n["count_depth"] = d; }); tree.resort_children (function (a,b) { return (a["count_depth"] - b["count_depth"]) * (asc ? 1 : -1); }); } sort_nodes (true); tree.traverse_and_compute ((n) => { //if (!tree.is_leafnode (n) && !n.tagged_view && n.parent && n.parent.tagged_view) { //n.notshown = true; //} }); t.placenodes(); t.update(); return t; }31:[] 2d:{"title":"Interactive Protein Selection Analysis","cells":[{"id":0,"value":"# Interactive Protein Selection Analysis","pinned":false,"hidden":false,"mode":"md"},{"id":13,"value":"{Description}
\n\nDesigned for use in concert with AOC and AMES.\n\nFor this notebook the data is from:
\nhttps://github.com/aglucaci/AOC-REM2
\nhttps://github.com/aglucaci/AMES-REM2
\n","pinned":false,"hidden":false,"mode":"md"},{"id":437,"value":"## Alignment Visualization","pinned":false,"hidden":false,"mode":"md"},{"id":501,"value":"fullscreen2 = {\n const button = html`