slowkow/mygene.html

## mygene.html
<!DOCTYPE HTML>
<html>

<head>

<meta http-equiv="Content-Type" content="text/html; charset=utf-8">

<script src="//ajax.googleapis.com/ajax/libs/jquery/1.11.1/jquery.min.js"></script>
<script type="text/javascript" src="js/typeahead.bundle.min.js"></script>

<title>Gene autocomplete</title>

<style>

p {
  line-height: 160%;
}

#scrollable-dropdown-menu {
  text-align: center;
}

input {
  padding: 1em;
  min-width: 400px;
}

#savedResults {
  max-width: 900px;
  margin: 80px auto;
}

#savedResult {
  padding: 8px 12px;
  margin: 20px 0px;
  font-size: 18px;
  line-height: 20px;
  padding: 12px 12px;
  border: 2px solid #ccc;
  -webkit-border-radius: 8px;
     -moz-border-radius: 8px;
          border-radius: 8px;
  outline: none;
}

#input-container {
  margin-top: 5em;
}

.tt-dropdown-menu {
  text-align: left;
  min-width: 400px;
}

.typeahead,
.tt-query,
.tt-hint {
  width: 420px;
  height: 30px;
  padding: 8px 12px;
  font-size: 24px;
  line-height: 30px;
  border: 2px solid #ccc;
  -webkit-border-radius: 8px;
     -moz-border-radius: 8px;
          border-radius: 8px;
  outline: none;
}

.typeahead {
  background-color: #fff;
}

.typeahead:focus {
  border: 2px solid #0097cf;
}

.tt-query {
  -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075);
     -moz-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075);
          box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075);
}

.tt-hint {
  color: #999
}

.tt-dropdown-menu {
  width: 480px;
  margin-top: 12px;
  padding: 8px 0;
  background-color: #fff;
  border: 1px solid #ccc;
  border: 1px solid rgba(0, 0, 0, 0.2);
  -webkit-border-radius: 8px;
     -moz-border-radius: 8px;
          border-radius: 8px;
  -webkit-box-shadow: 0 5px 10px rgba(0,0,0,.2);
     -moz-box-shadow: 0 5px 10px rgba(0,0,0,.2);
          box-shadow: 0 5px 10px rgba(0,0,0,.2);
}

.tt-suggestion {
  padding: 3px 20px;
  font-size: 18px;
  line-height: 24px;
}

.tt-suggestion.tt-cursor {
  color: #fff;
  background-color: #0097cf;
}

.tt-suggestion p {
  margin: 0;
}

</style>

</head>

<body>

<a href="https://gist.github.com/slowkow/99052cd3c8a517254524"><img style="position: absolute; top: 0; left: 0; border: 0;" src="https://camo.githubusercontent.com/82b228a3648bf44fc1163ef44c62fcc60081495e/68747470733a2f2f73332e616d617a6f6e6177732e636f6d2f6769746875622f726962626f6e732f666f726b6d655f6c6566745f7265645f6161303030302e706e67" alt="Fork me on GitHub" data-canonical-src="https://s3.amazonaws.com/github/ribbons/forkme_left_red_aa0000.png"></a>

<div id="input-container">
  <div id="scrollable-dropdown-menu">
    <input class="typeahead" type="text" placeholder="HLA-B">
  </div>
</div>

<div id="savedResults"></div>

<script>

var numberWithCommas = function(x) {
  return x.toString().replace(/\B(?=(\d{3})+(?!\d))/g, ",");
}

var format = function(form, datum) {
  return form.replace(/{([^}]+)}/g, function(match, key) {
    return typeof datum[key] != 'undefined' ? datum[key] : '';
  });
};

var posToRegion = function(pos) {
  if (pos['chr'] && pos['start'] && pos['end']) {
    return pos['chr'] + ':' +
      numberWithCommas(pos['start']) + '-' +
      numberWithCommas(pos['end']);
  }
  return '';
}

var entrezGeneLink = function(datum) {
  var form = 'Entrez: ' +
    '<a href="http://www.ncbi.nlm.nih.gov/gene/{entrezgene}">' +
    '{entrezgene}</a>';
  if (datum['entrezgene']) {
    return format(form, datum);
  }
  return '';
}

var hgncGeneLink = function(datum) {
  var form = 'HGNC: ' +
    '<a href="http://www.genenames.org/cgi-bin/gene_symbol_report' +
    '?hgnc_id=HGNC:{HGNC}">{HGNC}</a>';
  if (datum['HGNC']) {
    return format(form, datum);
  }
  return '';
}

var jbrowseRegionLink = function(pos) {
  var url = 'http://www.broadinstitute.org/~slowikow/JBrowse-1.10.1/' +
    '?loc={chr}%3A{start}..{end}' +
    '&tracks=Adipose%20-%20Subcutaneous%2CWhole%20Blood' +
    '%2CArtery%20-%20Aorta%2CMuscle%20-%20Skeletal' +
    '%2CBrain%20-%20Hippocampus%2CPituitary' +
    '%2CSkin%20-%20Sun%20Exposed%20(Lower%20leg)%2CStomach' +
    '%2CPancreas%2CColon%20-%20Transverse' +
    '%2CEnsembl%20v72%20Transcripts';
  var form = 'GTEx: <a href="' + url + '">{chr}:{start}-{end}</a>';
  if (pos['chr'] && pos['start'] && pos['end']) {
    return format(form, pos);
  }
  return '';
}

var ucscRegionLink = function(pos) {
  var form = 'UCSC: ' +
    '<a href="https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19' +
    '&position=chr{chr}%3A{start}-{end}">' +
    '{chr}:{start}-{end}</a>';
  if (pos['chr'] && pos['start'] && pos['end']) {
    return format(form, pos);
  }
  return '';
}

var gtexRegionLink = function(pos) {
  var form = 'GTEx: ' +
    'http://epigenomegateway.wustl.edu/browser/' +
    '?genome=hg19&coordinate=chr7:26663835-28123541';
}

var formatSuggestion = function(datum) {
  var pos = datum['genomic_pos_hg19'];
  var region = '';
  if (pos) {
    if (pos.length > 1) {
      pos = pos[0];
    }
    region = ucscRegionLink(pos);
  }
  var space = '&nbsp;&nbsp;&nbsp;&nbsp;';
  var form = '<div><strong>{symbol}</strong>' +
    ' <span style="font-size:80%">' + space + region + space +
    hgncGeneLink(datum) + '</span>' +
    '<br>{name}</div>';
    //' Entrez: <a href="http://www.ncbi.nlm.nih.gov/gene/{entrezgene}">{entrezgene}</a>' +
  return format(form, datum);
}

var formatSavedResult = function(datum) {
  var form =
    '<div id="savedResult"><strong>{symbol}</strong>' +
    '&nbsp;&nbsp;' + hgncGeneLink(datum) +
    '<br><p><em>{name}</em></p>';
  var pos = datum['genomic_pos_hg19'];
  if (pos) {
    if (pos.length > 1) {
      pos = pos[0];
    }
    form += '<p>' + ucscRegionLink(pos) +
      '&nbsp;&nbsp;' + jbrowseRegionLink(pos) + '</p>';
  }
  form += '<p>{summary}</p></div>';
  return format(form, datum);
}

var engine = new Bloodhound({
  name: 'genes',
  limit: 15,
  remote: {
    url: 'http://mygene.info/v2/query?q=%QUERY*' +
      '&fields=symbol,name,entrezgene,summary,genomic_pos_hg19,HGNC' +
      '&species=human&size=15' +
      '&email=slowikow@broadinstitute.org',
    filter: function(datum) {
      return datum['hits'];
    }
  },
  datumTokenizer: function(datum) {
    return Bloodhound.tokenizers.whitespace(datum.val);
  },
  queryTokenizer: Bloodhound.tokenizers.whitespace
});

var promise = engine.initialize();

promise
.done(function() { console.log('success!'); })
.fail(function() { console.log('err!'); });

$('.typeahead').typeahead(null, {
  name: 'genes',
  displayKey: 'symbol',
  source: engine.ttAdapter(),
  templates: {
    suggestion: formatSuggestion
  }
});

$('.typeahead').on('typeahead:selected', function(obj, datum, name) {
  console.log(datum);
  $("#savedResults").prepend(formatSavedResult(datum));
});

</script>

</body>

</html>
	<!DOCTYPE HTML>
	<html>

	<head>

	<meta http-equiv="Content-Type" content="text/html; charset=utf-8">

	<script src="//ajax.googleapis.com/ajax/libs/jquery/1.11.1/jquery.min.js"></script>
	<script type="text/javascript" src="js/typeahead.bundle.min.js"></script>

	<title>Gene autocomplete</title>

	<style>

	p {
	line-height: 160%;
	}

	#scrollable-dropdown-menu {
	text-align: center;
	}

	input {
	padding: 1em;
	min-width: 400px;
	}

	#savedResults {
	max-width: 900px;
	margin: 80px auto;
	}

	#savedResult {
	padding: 8px 12px;
	margin: 20px 0px;
	font-size: 18px;
	line-height: 20px;
	padding: 12px 12px;
	border: 2px solid #ccc;
	-webkit-border-radius: 8px;
	-moz-border-radius: 8px;
	border-radius: 8px;
	outline: none;
	}

	#input-container {
	margin-top: 5em;
	}

	.tt-dropdown-menu {
	text-align: left;
	min-width: 400px;
	}

	.typeahead,
	.tt-query,
	.tt-hint {
	width: 420px;
	height: 30px;
	padding: 8px 12px;
	font-size: 24px;
	line-height: 30px;
	border: 2px solid #ccc;
	-webkit-border-radius: 8px;
	-moz-border-radius: 8px;
	border-radius: 8px;
	outline: none;
	}

	.typeahead {
	background-color: #fff;
	}

	.typeahead:focus {
	border: 2px solid #0097cf;
	}

	.tt-query {
	-webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075);
	-moz-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075);
	box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075);
	}

	.tt-hint {
	color: #999
	}

	.tt-dropdown-menu {
	width: 480px;
	margin-top: 12px;
	padding: 8px 0;
	background-color: #fff;
	border: 1px solid #ccc;
	border: 1px solid rgba(0, 0, 0, 0.2);
	-webkit-border-radius: 8px;
	-moz-border-radius: 8px;
	border-radius: 8px;
	-webkit-box-shadow: 0 5px 10px rgba(0,0,0,.2);
	-moz-box-shadow: 0 5px 10px rgba(0,0,0,.2);
	box-shadow: 0 5px 10px rgba(0,0,0,.2);
	}

	.tt-suggestion {
	padding: 3px 20px;
	font-size: 18px;
	line-height: 24px;
	}

	.tt-suggestion.tt-cursor {
	color: #fff;
	background-color: #0097cf;
	}

	.tt-suggestion p {
	margin: 0;
	}

	</style>

	</head>

	<body>

	<a href="https://gist.github.com/slowkow/99052cd3c8a517254524"><img style="position: absolute; top: 0; left: 0; border: 0;" src="https://camo.githubusercontent.com/82b228a3648bf44fc1163ef44c62fcc60081495e/68747470733a2f2f73332e616d617a6f6e6177732e636f6d2f6769746875622f726962626f6e732f666f726b6d655f6c6566745f7265645f6161303030302e706e67" alt="Fork me on GitHub" data-canonical-src="https://s3.amazonaws.com/github/ribbons/forkme_left_red_aa0000.png"></a>

	<div id="input-container">
	<div id="scrollable-dropdown-menu">
	<input class="typeahead" type="text" placeholder="HLA-B">
	</div>
	</div>

	<div id="savedResults"></div>

	<script>

	var numberWithCommas = function(x) {
	return x.toString().replace(/\B(?=(\d{3})+(?!\d))/g, ",");
	}

	var format = function(form, datum) {
	return form.replace(/{([^}]+)}/g, function(match, key) {
	return typeof datum[key] != 'undefined' ? datum[key] : '';
	});
	};

	var posToRegion = function(pos) {
	if (pos['chr'] && pos['start'] && pos['end']) {
	return pos['chr'] + ':' +
	numberWithCommas(pos['start']) + '-' +
	numberWithCommas(pos['end']);
	}
	return '';
	}

	var entrezGeneLink = function(datum) {
	var form = 'Entrez: ' +
	'<a href="http://www.ncbi.nlm.nih.gov/gene/{entrezgene}">' +
	'{entrezgene}</a>';
	if (datum['entrezgene']) {
	return format(form, datum);
	}
	return '';
	}

	var hgncGeneLink = function(datum) {
	var form = 'HGNC: ' +
	'<a href="http://www.genenames.org/cgi-bin/gene_symbol_report' +
	'?hgnc_id=HGNC:{HGNC}">{HGNC}</a>';
	if (datum['HGNC']) {
	return format(form, datum);
	}
	return '';
	}

	var jbrowseRegionLink = function(pos) {
	var url = 'http://www.broadinstitute.org/~slowikow/JBrowse-1.10.1/' +
	'?loc={chr}%3A{start}..{end}' +
	'&tracks=Adipose%20-%20Subcutaneous%2CWhole%20Blood' +
	'%2CArtery%20-%20Aorta%2CMuscle%20-%20Skeletal' +
	'%2CBrain%20-%20Hippocampus%2CPituitary' +
	'%2CSkin%20-%20Sun%20Exposed%20(Lower%20leg)%2CStomach' +
	'%2CPancreas%2CColon%20-%20Transverse' +
	'%2CEnsembl%20v72%20Transcripts';
	var form = 'GTEx: <a href="' + url + '">{chr}:{start}-{end}</a>';
	if (pos['chr'] && pos['start'] && pos['end']) {
	return format(form, pos);
	}
	return '';
	}

	var ucscRegionLink = function(pos) {
	var form = 'UCSC: ' +
	'<a href="https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19' +
	'&position=chr{chr}%3A{start}-{end}">' +
	'{chr}:{start}-{end}</a>';
	if (pos['chr'] && pos['start'] && pos['end']) {
	return format(form, pos);
	}
	return '';
	}

	var gtexRegionLink = function(pos) {
	var form = 'GTEx: ' +
	'http://epigenomegateway.wustl.edu/browser/' +
	'?genome=hg19&coordinate=chr7:26663835-28123541';
	}

	var formatSuggestion = function(datum) {
	var pos = datum['genomic_pos_hg19'];
	var region = '';
	if (pos) {
	if (pos.length > 1) {
	pos = pos[0];
	}
	region = ucscRegionLink(pos);
	}
	var space = '    ';
	var form = '<div><strong>{symbol}</strong>' +
	' <span style="font-size:80%">' + space + region + space +
	hgncGeneLink(datum) + '</span>' +
	'<br>{name}</div>';
	//' Entrez: <a href="http://www.ncbi.nlm.nih.gov/gene/{entrezgene}">{entrezgene}</a>' +
	return format(form, datum);
	}

	var formatSavedResult = function(datum) {
	var form =
	'<div id="savedResult"><strong>{symbol}</strong>' +
	'  ' + hgncGeneLink(datum) +
	'<br><p><em>{name}</em></p>';
	var pos = datum['genomic_pos_hg19'];
	if (pos) {
	if (pos.length > 1) {
	pos = pos[0];
	}
	form += '<p>' + ucscRegionLink(pos) +
	'  ' + jbrowseRegionLink(pos) + '</p>';
	}
	form += '<p>{summary}</p></div>';
	return format(form, datum);
	}

	var engine = new Bloodhound({
	name: 'genes',
	limit: 15,
	remote: {
	url: 'http://mygene.info/v2/query?q=%QUERY*' +
	'&fields=symbol,name,entrezgene,summary,genomic_pos_hg19,HGNC' +
	'&species=human&size=15' +
	'&email=slowikow@broadinstitute.org',
	filter: function(datum) {
	return datum['hits'];
	}
	},
	datumTokenizer: function(datum) {
	return Bloodhound.tokenizers.whitespace(datum.val);
	},
	queryTokenizer: Bloodhound.tokenizers.whitespace
	});

	var promise = engine.initialize();

	promise
	.done(function() { console.log('success!'); })
	.fail(function() { console.log('err!'); });

	$('.typeahead').typeahead(null, {
	name: 'genes',
	displayKey: 'symbol',
	source: engine.ttAdapter(),
	templates: {
	suggestion: formatSuggestion
	}
	});

	$('.typeahead').on('typeahead:selected', function(obj, datum, name) {
	console.log(datum);
	$("#savedResults").prepend(formatSavedResult(datum));
	});

	</script>

	</body>

	</html>