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example-peff-reader.html
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example-peff-reader.html
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<html>
<head>
<title>pViz PEFF reader</title>
<link rel="stylesheet" type="text/css" href="deps/bootstrap.min.css">
<link rel="stylesheet" type="text/css" href="deps/pviz-core.css">
<script src="deps/pviz-bundle.min.js"></script>
<!-- just a few lines of javscript to decorate the page -->
<script src="examples-utils.js"></script>
</head>
<body class="container">
<div class="row">
<h2>pViz PEFF reader example</h2>
</div>
<div id="main" class="row"></div>
<div class="row">
<h3>Comments</h3>
Peff format extends fasta with entry annotations. some of them are positional.
<pre>var cont = 'nxp:NX_Q16586-1 \\DbUniqueId=NX_Q16586-1 \\Pname=Alpha-sarcoglycan isoform SGCA-1 \\Gname=SGCA \\NcbiTaxId=9606 \\TaxName=Homo Sapiens \\Length=387 \\SV=55 \\EV=119 \\PE=1 \\ModRes=(174|N-linked (GlcNAc...))(246|N-linked (GlcNAc...)) \\Variant=(30|30|L)(31|31|P)(34|34|C)(34|34|H)(62|62|H)(68|68|E)(74|74|W)(77|77|C)(89|89|P)(91|91|R)(93|93|V)(97|97|G)(98|98|H)(98|98|C)(103|103|T)(107|107|V)(110|110|Q)(124|124|T)(136|136|APGAQP)(137|137|K)(137|137|G)(158|158|F)(173|173|P)(175|175|A)(190|190|D)(196|196|I)(201|201|D)(205|205|H)(221|221|H)(228|228|Q)(242|242|A)(247|247|M)(284|284|C)(310|310|C)(374|374|C) \\Processed=(1|23|signal peptide)(24|387|mature protein)
MAETLFWTPLLVVLLAGLGDTEAQQTTLHPLVGRVFVHTLDHETFLSLPEHVAVPPAVHI
TYHAHLQGHPDLPRWLRYTQRSPHHPGFLYGSATPEDRGLQVIEVTAYNRDSFDTTRQRL
VLEIGDPEGPLLPYQAEFLVRSHDAEEVLPSTPASRFLSALGGLWEPGELQLLNVTSALD
RGGRVPLPIEGRKEGVYIKVGSASPFSTCLKMVASPDSHARCAQGQPPLLSCYDTLAPHF
RVDWCNVTLVDKSVPEPADEVPTPGDGILEHDPFFCPPTEAPDRDFLVDALVTLLVPLLV
ALLLTLLLAYVMCCRREGRLKRDLATSDIQMVHHCTIHGNTEELRQMAASREVPRPLSTL
PMFNVHTGERLPPRVDSAQVPLILDQH
</pre>
</div>
<script class="example">
//namespace handling pViz classes
var pviz = this.pviz;
var cont = 'nxp:NX_Q16586-1 \\DbUniqueId=NX_Q16586-1 \\Pname=Alpha-sarcoglycan isoform SGCA-1 \\Gname=SGCA \\NcbiTaxId=9606 \\TaxName=Homo Sapiens \\Length=387 \\SV=55 \\EV=119 \\PE=1 \\ModRes=(174|N-linked (GlcNAc...))(246|N-linked (GlcNAc...)) \\Variant=(30|30|L)(31|31|P)(34|34|C)(34|34|H)(62|62|H)(68|68|E)(74|74|W)(77|77|C)(89|89|P)(91|91|R)(93|93|V)(97|97|G)(98|98|H)(98|98|C)(103|103|T)(107|107|V)(110|110|Q)(124|124|T)(136|136|APGAQP)(137|137|K)(137|137|G)(158|158|F)(173|173|P)(175|175|A)(190|190|D)(196|196|I)(201|201|D)(205|205|H)(221|221|H)(228|228|Q)(242|242|A)(247|247|M)(284|284|C)(310|310|C)(374|374|C) \\Processed=(1|23|signal peptide)(24|387|mature protein)\n\
MAETLFWTPLLVVLLAGLGDTEAQQTTLHPLVGRVFVHTLDHETFLSLPEHVAVPPAVHI\n\
TYHAHLQGHPDLPRWLRYTQRSPHHPGFLYGSATPEDRGLQVIEVTAYNRDSFDTTRQRL\n\
VLEIGDPEGPLLPYQAEFLVRSHDAEEVLPSTPASRFLSALGGLWEPGELQLLNVTSALD\n\
RGGRVPLPIEGRKEGVYIKVGSASPFSTCLKMVASPDSHARCAQGQPPLLSCYDTLAPHF\n\
RVDWCNVTLVDKSVPEPADEVPTPGDGILEHDPFFCPPTEAPDRDFLVDALVTLLVPLLV\n\
ALLLTLLLAYVMCCRREGRLKRDLATSDIQMVHHCTIHGNTEELRQMAASREVPRPLSTL\n\
PMFNVHTGERLPPRVDSAQVPLILDQH\n\
'
var fastaReader=new pviz.FastaReader()
var entry = fastaReader.buildSeqEntry(cont)
new pviz.SeqEntryAnnotInteractiveView({
model : entry,
el : '#main'
}).render();
</script>
</body>
</html>