forked from dasmoth/dalliance
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathtest.html
171 lines (156 loc) · 8.34 KB
/
test.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
<!DOCTYPE html>
<html>
<head>
<style>
</style>
<title>Human NCBI36 :: Dalliance</title>
<script language="javascript" src="node_modules/es6-promise/dist/promise-0.1.2.js"></script>
<script language="javascript" src="js/bam.js"></script>
<script language="javascript" src="js/bigwig.js"></script>
<script language="javascript" src="js/das.js"></script>
<script language="javascript" src="js/spans.js"></script>
<script language="javascript" src="js/utils.js"></script>
<script language="javascript" src="js/cbrowser.js"></script>
<script language="javascript" src="js/feature-popup.js"></script>
<script language="javascript" src="js/tier.js"></script>
<script language="javascript" src="js/features.js"></script>
<script language="javascript" src="js/color.js"></script>
<script language="javascript" src="js/feature-draw.js"></script>
<script language="javascript" src="js/sequence-draw.js"></script>
<script language="javascript" src="js/domui.js"></script>
<script language="javascript" src="js/track-adder.js"></script>
<script language="javascript" src="js/chainset.js"></script>
<script language="javascript" src="js/version.js"></script>
<script language="javascript" src="js/sha1.js"></script>
<script language="javascript" src="js/sample.js"></script>
<script language="javascript" src="js/kspace.js"></script>
<script language="javascript" src="js/bin.js"></script>
<script language="javascript" src="js/twoBit.js"></script>
<script language="javascript" src="js/thub.js"></script>
<script language="javascript" src="js/svg-export.js"></script>
<script language="javascript" src="node_modules/jszlib/js/inflate.js"></script>
<script language="javascript" src="js/browser-ui.js"></script>
<script language="javascript" src="js/glyphs.js"></script>
<script language="javascript" src="js/session.js"></script>
<script language="javascript" src="js/jbjson.js"></script>
<script language="javascript" src="js/sourceadapters.js"></script>
<script language="javascript" src="polyfills/html5slider.js"></script>
<script language="javascript" src="js/ensembljson.js"></script>
<script language="javascript" src="js/overlay.js"></script>
<script language="javascript" src="js/tier-actions.js"></script>
<script language="javascript" src="js/tier-edit.js"></script>
<script language="javascript" src="js/search.js"></script>
<script language="javascript" src="js/tabix.js"></script>
<script language="javascript" src="js/tabix-source.js"></script>
<script language="javascript" src="js/bigtab.js"></script>
<script language="javascript" src="js/memstore.js"></script>
<script language="javascript" src="js/vcf.js"></script>
<script language="javascript" src="js/bedwig.js"></script>
<script language="javascript" src="js/probe.js"></script>
<script language="javascript" src="js/trix.js"></script>
<script language="javascript" src="js/export-ui.js"></script>
<script language="javascript" src="js/export-config.js"></script>
<script language="javascript" src="js/lh3utils.js"></script>
<script language="javascript" src="js/svg-utils.js"></script>
<script language="javascript" src="js/numformats.js"></script>
<script language="javascript" src="js/cigar.js"></script>
<script language="javascript" src="js/style.js"></script>
<script language="javascript">
var b = new Browser({
chr: '22',
viewStart: 30000000,
viewEnd: 30030000,
cookieKey: 'human2',
coordSystem: {
speciesName: 'Human',
taxon: 9606,
auth: 'NCBI',
version: 36
},
chains: {
hg19ToHg18: new Chainset('http://www.derkholm.net:8080/das/hg19ToHg18/', 'GRCh37', 'NCBI36',
{
speciesName: 'Human',
taxon: 9606,
auth: 'GRCh',
version: 37
})
},
sources: [{name: 'Genome',
twoBitURI: 'http://www.biodalliance.org/datasets/hg18.2bit',
// uri: 'http://www.derkholm.net:8080/das/hsa_54_36p/',
tier_type: 'sequence'},
{name: 'e! transcripts',
uri: 'http://beta.rest.ensembl.org',
tier_type: 'ensembl',
species: 'human',
type: ['transcript', 'exon', 'cds'],
mapping: 'hg19ToHg18',
},
{name: 'Genes',
desc: 'Gene structures from Ensembl 54',
uri: 'http://www.derkholm.net:8080/das/hsa_54_36p/',
collapseSuperGroups: true,
provides_karyotype: true,
provides_search: true,
provides_entrypoints: true,
maxbins: false,
featureInfoPlugin: function(f, info) {
info.add('Testing', 'This is another test!');
}
},
{name: 'Repeats',
uri: 'http://www.derkholm.net:8080/das/hsa_54_36p/',
stylesheet_uri: 'http://www.biodalliance.org/stylesheets/repeats-L1.xml'},
{name: 'CpG Density',
uri: 'http://www.derkholm.net:8080/das/hg18comp/',
// stylesheet_uri: 'http://www.biodalliance.org/stylesheets/cpg-hist.xml',
quantLeapThreshold: 0.8,
forceReduction: -1,
style: [{type: 'cpgoe',
style: {glyph: 'LINEPLOT',
FGCOLOR: 'green', HEIGHT: '50', MIN: 0, MAX: 1.2}}]},
{name: 'MeDIP-raw',
desc: 'MeDIP-seq reads from Nature Biotech. 26:779-785',
uri: 'http://www.derkholm.net:8080/das/medipseq_reads/',
group: 'Custom group'},
{name: 'BWG test',
bwgURI: 'http://www.biodalliance.org/datasets/spermMethylation.bw',
stylesheet_uri: 'http://www.ebi.ac.uk/das-srv/genomicdas/das/batman_seq_SP/stylesheet',
quantLeapThreshold: 80}
/* ,{name: 'BBD test',
bwgURI: 'http://www.biodalliance.org/datasets/ensGene.bb',
link: 'http://ncbi36.ensembl.org/Homo_sapiens/Gene/Summary?t=$$',
collapseSuperGroups: true,
disable: true} */
,{name: 'Style test',
uri: './glyph-test/',
features_uri: './glyph-test/features.xml',
stylesheet_uri: './glyph-test/stylesheet.xml',
dasStaticFeatures: true,
disabled: true}
,{name: 'BWG hist',
bwgURI: 'http://www.biodalliance.org/datasets/spermMethylation.bw',
style: [{type: 'default',
style: {glyph: 'HISTOGRAM', HEIGHT: 50 /* , MIN: 0, MAX: 100 */}}],
quantLeapThreshold: 80}
],
setDocumentTitle: true,
uiPrefix: '',
searchEndpoint: new DASSource('http://www.derkholm.net:8080/das/hsa_54_36p/'),
browserLinks: {
Ensembl: 'http://ncbi36.ensembl.org/Homo_sapiens/Location/View?r=${chr}:${start}-${end}',
UCSC: 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr${chr}:${start}-${end}',
Sequence: 'http://www.derkholm.net:8080/das/hg18comp/sequence?segment=${chr}:${start},${end}'
}
});
b.hubs = ['http://www.biodalliance.org/datasets/testhub/hub.txt'];
b.addFeatureInfoPlugin(function(f, info) {
info.add('Testing', 'This is a test!');
});
</script>
</head>
<body>
<div id='svgHolder'>Dalliance genome browser goes here. Unless you have an ancient web browser or something.</div>
</body>
</html>