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Completion of Variant Call Adjacency Matrix #1

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Completion of Variant Call Adjacency Matrix #1

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dc6a533
Example skeleton
david4096 Jun 22, 2016
fb665c0
Add files via upload
achave11-ucsc Jun 24, 2016
7c0a60e
Update requirements
david4096 Jun 29, 2016
897747e
first commit of variantMatrix
Jun 29, 2016
0c4cb32
visualized variant occurence graph
Jul 5, 2016
f1ca8a0
added mean computation function
Jul 6, 2016
52cfebf
added kmeans clustering on the variant matrix
Jul 15, 2016
3c0fb1e
population frequencies have been graphed
Aug 18, 2016
48180a2
cleaned up variant matrix notebook
Feb 2, 2017
d2a8320
Update variantMatrix.ipynb
Feb 7, 2017
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36 changes: 36 additions & 0 deletions html/js_examples.html
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Original file line number Diff line number Diff line change
@@ -0,0 +1,36 @@
<html>
<head>
<script src="https://code.jquery.com/jquery-1.12.3.min.js" integrity="sha256-aaODHAgvwQW1bFOGXMeX+pC4PZIPsvn2h1sArYOhgXQ=" crossorigin="anonymous"></script>
</head>
<body>
<script>
var baseurl = "http://1kgenomes.ga4gh.org/";

function getVariants(query, callback) {
return $.ajax(baseurl + "variants/search", {
data : JSON.stringify(query),
contentType : 'application/json',
type : 'POST',
success: callback,
dataType: 'json'
});
}
console.log('hi');

var variantSetId = "WyIxa2dlbm9tZXMiLCJ2cyIsInJlbGVhc2UiXQ";

var query = {
"variantSetId": variantSetId,
"referenceName": "1",
"start": 0,
"end": 123123123123
}

function myCallback(response) {
console.log(response);
}

getVariants(query, myCallback);
</script>
</body>
</html>
Binary file added python_notebooks/Cigar-Notes : ClipSoft.png
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2 changes: 1 addition & 1 deletion python_notebooks/pileup.ipynb
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Expand Up @@ -237,4 +237,4 @@
},
"nbformat": 4,
"nbformat_minor": 0
}
}
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