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update gene page and gene orientation motifs (same but alphabetically…
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… first permutation)
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@hdashnow
hdashnow committed Oct 30, 2024
1 parent b42dbde commit 6a49d7f
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Showing 2 changed files with 88 additions and 21 deletions.
6 changes: 3 additions & 3 deletions data/STRchive-database.json
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Original file line number Diff line number Diff line change
Expand Up @@ -3296,11 +3296,11 @@
"gene_strand":"+",
"reference_motif_reference_orientation":"TTTTA",
"pathogenic_motif_reference_orientation":"TTTCA",
"pathogenic_motif_gene_orientation":"TTTCA",
"pathogenic_motif_gene_orientation":"ATTTC",
"benign_motif_reference_orientation":"TTTTA",
"benign_motif_gene_orientation":"TTTTA",
"benign_motif_gene_orientation":"ATTTT",
"unknown_motif_reference_orientation":"GGGGT,GGGAT",
"unknown_motif_gene_orientation":"GGGGT,GGGAT",
"unknown_motif_gene_orientation":"GGGGT,ATGGG",
"disease":"Familial adult myoclonic epilepsy type 8",
"gene":"RAI1",
"flank_motif":null,
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103 changes: 85 additions & 18 deletions database/RAI1.html
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Original file line number Diff line number Diff line change
Expand Up @@ -227,7 +227,6 @@ <h4>Locus</h4>
}
locus_html = locus_html +
`
<li><b>Type:</b> ${f.type}</li>
<li><b>Reference motif:</b> ${f.reference_motif_reference_orientation}</li>
</div>
</div>
Expand All @@ -237,7 +236,6 @@ <h4>Locus</h4>
<h4>Disease</h4>
<div class="ui list">
<li><b>ID:</b> ${f.disease_id}</li>
<li><b>Description:</b> ${f.disease}</li>
<li><b>Inheritance:</b> ${inheritance_desc}</li>`
};

Expand Down Expand Up @@ -297,6 +295,9 @@ <h4>Disease</h4>
}
};

locus_html = locus_html +
`<li>${f.disease_description}</li>`

locus_html = locus_html +
`
</div>
Expand Down Expand Up @@ -384,19 +385,76 @@ <h4>Alleles</h4>
<div class="column">
<div class="ui segment">
<h4>Resources</h4>
<h4>Tandem Repeat Resources</h4>
<div class="ui list">`

if (f.gnomAD_gene != '') {
locus_html = locus_html +
`<li><b>gnomAD:</b> <a href="https://gnomad.broadinstitute.org/short-tandem-repeat/${f.gnomAD_gene}?dataset=gnomad_r3">${f.gnomAD_gene}</a></li>`
};

if (f.TRgnomAD != '') {
locus_html = locus_html +
`<li><b>TR-gnomAD:</b> <a href="https://wlcb.oit.uci.edu/TRgnomAD/Distribution.php?index_id=${f.TRgnomAD}">${f.TRgnomAD}</a></li>`
};

if (f.STRipy_gene != '') {
locus_html = locus_html +
`<li><b>STRipy:</b> <a href="https://stripy.org/database/${f.STRipy_gene}">${f.STRipy_gene}</a></li>`
};

if (f.WebSTR_hg38 != '' | f.WebSTR_hg19 != '') {
locus_html = locus_html + `<li><b>WebSTR:</b>
<ul>`
if (f.WebSTR_hg19 != '') {
locus_html = locus_html + `<li><b>hg19:</b> `
f.WebSTR_hg19.split(";").forEach(function (WebSTR_hg19_ID) {
locus_html = locus_html +
`<a href="https://webstr.ucsd.edu/locus?repeat_id=${WebSTR_hg19_ID.trim()}">${WebSTR_hg19_ID}</a>`
})
locus_html = locus_html + `</li>`
}
if (f.WebSTR_hg38 != '') {
locus_html = locus_html + `<li><b>hg38:</b> `
f.WebSTR_hg38.split(";").forEach(function (WebSTR_hg38_ID) {
locus_html = locus_html +
`<a href="https://webstr.ucsd.edu/locus?repeat_id=${WebSTR_hg38_ID.trim()}&genome=hg38">${WebSTR_hg38_ID}</a>`
})
locus_html = locus_html + `</li>`
}

locus_html = locus_html + `</ul>`
};

if (f.source != '') {
locus_html = locus_html + `<li><b>Sources reviewed for STRchive:</b></li>
`
f.source.split(", ").forEach(function (source) {
if (source.startsWith("http")) {
locus_html = locus_html +
`<li><a href="${source.trim()}">${source}</a></li>`
}
else {
locus_html = locus_html +
`<li><a href="https://www.google.com/search?q=${source.trim()}">${source}</a></li>`
}

})

};
locus_html = locus_html +
`
</div>
</div>
</div>`

locus_html = locus_html +
`
<div class="column">
<div class="ui segment">
<h4>Disease Resources</h4>
<div class="ui list">`

if (f.OMIM != '') {
locus_html = locus_html + `<li><b>OMIM:</b> `
f.OMIM.split(";").forEach(function (OMIMid) {
Expand All @@ -421,28 +479,37 @@ <h4>Resources</h4>
})
locus_html = locus_html + `</li>`
};
if (f.source != '') {
locus_html = locus_html + `<li><b>Sources reviewed for STRchive:</b></li>
`
f.source.split(", ").forEach(function (source) {
if (source.startsWith("http")) {
locus_html = locus_html +
`<li><a href="${source.trim()}">${source}</a></li>`
}
else {
locus_html = locus_html +
`<li><a href="https://www.google.com/search?q=${source.trim()}">${source}</a></li>`
}

if (f.MedGen != '') {
locus_html = locus_html + `<li><b>MedGen:</b> `
f.MedGen.split(";").forEach(function (MedGenID) {
locus_html = locus_html +
`<a href="https://www.ncbi.nlm.nih.gov/medgen/?term=${MedGenID.trim()}">${MedGenID}</a>`
})

locus_html = locus_html + `</li>`
};
if (f.Orphanet != '') {
locus_html = locus_html + `<li><b>Orphanet:</b> `
f.Orphanet.split(";").forEach(function (OrphanetID) {
locus_html = locus_html +
`<a href="https://www.orpha.net/en/disease/detail/${OrphanetID.trim()}">${OrphanetID}</a>`
})
locus_html = locus_html + `</li>`
};
if (f.GARD != '') {
locus_html = locus_html + `<li><b>GARD:</b> `
f.GARD.split(";").forEach(function (GARDid) {
locus_html = locus_html +
`<a href="https://rarediseases.info.nih.gov/diseases/${GARDid.trim()}/index">${GARDid}</a>`
})
locus_html = locus_html + `</li>`
};

locus_html = locus_html +
`
</div>
</div>
</div>`

if (f.details != '') {
locus_html = locus_html + `
<div class="ui column">
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