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Update GnomAD links
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@Char-Al
Char-Al committed Jan 17, 2024
1 parent 01661b7 commit 76c1486
Showing 1 changed file with 21 additions and 16 deletions.
37 changes: 21 additions & 16 deletions seal/templates/analysis/sample.html
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Original file line number Diff line number Diff line change
Expand Up @@ -474,8 +474,7 @@ <h3>Comments (<span class="commentsCountVar"></span>)</h3>
mobidetails = '<span onclick="openMD(\'' + data["annotations"]["HGVSc"] + '\')" class="fa-fw w3-text-flat-peter-river w3-hover-text-flat-carrot" style="cursor: pointer;"><span class="fa-layers"><i class="fas fa-bookmark"></i> <span class="fa-layers-text fa-inverse" data-fa-transform="shrink-10 up-2" style="font-weight:900">MD</span></span> MobiDetails</span> <br />'
}
franklin = '<a target="_blank" href="https://franklin.genoox.com/clinical-db/variant/snp/' + data["id"] + '" class="fa-layers fa-fw w3-text-flat-midnight-blue w3-hover-text-flat-wet-asphalt" style="cursor: pointer;"><span class="fa-layers"><i class="fas fa-bookmark"></i> <span class="fa-layers-text fa-inverse" data-fa-transform="shrink-10 up-2" style="font-weight:900">F</span></span> Franklin</a> ';
gnomad = '<a target="_blank" href="https://gnomad.broadinstitute.org/variant/' + data["id"] + '" class="fa-fw w3-text-indigo w3-hover-text-black" style="cursor: pointer;"><span class="fa-layers"><i class="fas fa-bookmark"></i> <span class="fa-layers-text fa-inverse" data-fa-transform="shrink-10 up-2" style="font-weight:900">G</span></span> GnomAD</a> ';
return "<div class='w3-tiny'>" + mobidetails + franklin + "<br />" + gnomad + "</div>";
return "<div class='w3-tiny'>" + mobidetails + franklin + "</div>";
}
}
},
Expand Down Expand Up @@ -701,41 +700,47 @@ <h3>Comments (<span class="commentsCountVar"></span>)</h3>
},
{% endfor %}
{
className: 'showTitle',
data: "annotations.gnomADg_AF",
className: '',
// data: "annotations.gnomADg_AF",
data: null,
render : {
_: function ( data, type, row, meta ) {
if(data != null) {
if (isNaN(parseFloat(data).toFixed(6))) {
if(data["annotations"]["gnomADg_AF"] != null) {
if (isNaN(parseFloat(data["annotations"]["gnomADg_AF"]).toFixed(6))) {
return null
}
return parseFloat(data).toFixed(6);
return parseFloat(data["annotations"]["gnomADg_AF"]).toFixed(6);
} else {
return null;
}
},
display: function ( data, type, row, meta ) {
if(data != null) {
if (isNaN(parseFloat(data).toFixed(6))) {
if(data["annotations"]["gnomADg_AF"] != null) {
if (isNaN(parseFloat(data["annotations"]["gnomADg_AF"]).toFixed(6))) {
return "<i>NA</i>"
}
gnomad = parseFloat(data);
gnomad = parseFloat(data["annotations"]["gnomADg_AF"]);
if (gnomad > 0.01) {
response = parseFloat(data).toFixed(4)
response = parseFloat(data["annotations"]["gnomADg_AF"]).toFixed(4)
} else {
response = parseFloat(data).toExponential(2)
response = parseFloat(data["annotations"]["gnomADg_AF"]).toExponential(2)
}
return "<span title='"+ gnomad +"'>" + response + "</span>";
gnomad_r = '<a target="_blank" href="https://gnomad.broadinstitute.org/variant/' + data["id"] + '?dataset=gnomad_r2_1" class="fa-fw w3-text-indigo w3-hover-text-black" style="cursor: pointer;"></span> '+ response+'</a> ';
gnomad1 = '<a title="ExAC" target="_blank" href="https://gnomad.broadinstitute.org/variant/' + data["id"] + '?dataset=exac" class="fa-fw w3-text-indigo w3-hover-text-black" style="cursor: pointer;"><span class="fa-layers"><i class="fas fa-bookmark"></i> <span class="fa-layers-text fa-inverse" data-fa-transform="shrink-10 up-2" style="font-weight:900">E</span></span></a> ';
gnomad2 = '<a title="GnomAD 2.1" target="_blank" href="https://gnomad.broadinstitute.org/variant/' + data["id"] + '?dataset=gnomad_r2_1" class="fa-fw w3-text-indigo w3-hover-text-black" style="cursor: pointer;"><span class="fa-layers"><i class="fas fa-bookmark"></i> <span class="fa-layers-text fa-inverse" data-fa-transform="shrink-10 up-2" style="font-weight:900">2</span></span></a> ';
gnomad3 = '<a title="GnomAD 3" target="_blank" href="https://gnomad.broadinstitute.org/variant/liftover/' + data["id"] + '/gnomad_r2_1/gnomad_r3" class="fa-fw w3-text-indigo w3-hover-text-black" style="cursor: pointer;"><span class="fa-layers"><i class="fas fa-bookmark"></i> <span class="fa-layers-text fa-inverse" data-fa-transform="shrink-10 up-2" style="font-weight:900">3</span></span></a> ';
gnomad4 = '<a title="GnomAD 4" target="_blank" href="https://gnomad.broadinstitute.org/variant/liftover/' + data["id"] + '/gnomad_r2_1/gnomad_r4" class="fa-fw w3-text-indigo w3-hover-text-black" style="cursor: pointer;"><span class="fa-layers"><i class="fas fa-bookmark"></i> <span class="fa-layers-text fa-inverse" data-fa-transform="shrink-10 up-2" style="font-weight:900">4</span></span></a> ';
return '<i title="' + gnomad + '">' + gnomad_r + '</i> <small>(v2.1)</small><br />' + gnomad1+ gnomad2+ gnomad3+ gnomad4;
} else {
return "<i>NA</i>";
}
},
sort: function ( data, type, row, meta ) {
if(data != null) {
if (isNaN(parseFloat(data).toFixed(6))) {
if(data["annotations"]["gnomADg_AF"] != null) {
if (isNaN(parseFloat(data["annotations"]["gnomADg_AF"]).toFixed(6))) {
return -0.5
}
return parseFloat(data).toFixed(6);
return parseFloat(data["annotations"]["gnomADg_AF"]).toFixed(6);
} else {
return -1
}
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