annotate test-data/blastxml/test.xml @ 3:7342f467507b draft

Uploaded v0.4 of JBrowse
author iuc
date Thu, 31 Dec 2015 13:58:43 -0500
parents
children ff11d442feed
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
2 <root>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
3 <metadata>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
4 <gencode>11</gencode>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
5 <genomes>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
6 <genome>test-data/merlin.fa</genome>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
7 </genomes>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
8 </metadata>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
9 <tracks>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
10 <track cat="Blah" format="blast">
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
11 <files>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
12 <trackFile path="test-data/blastxml/blast.xml" ext="blastxml" label="BlastP"/>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
13 </files>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
14
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
15 <options>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
16 <style>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
17 <className>feature</className>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
18 <description></description>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
19 <label>Description</label>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
20 <height>400px</height>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
21 </style>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
22 <blast>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
23 <parent>test-data/blastxml/merlin.gff</parent>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
24 <protein>true</protein>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
25 <min_gap>10</min_gap>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
26 </blast>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
27 <scaling>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
28 <method>score</method>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
29 <algo>blast</algo>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
30 <scales>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
31 <type>__auto__</type>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
32 </scales>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
33 <scheme>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
34 <type>opacity</type>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
35 <color>__auto__</color>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
36 </scheme>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
37 </scaling>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
38 </options>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
39 </track>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
40 <track cat="Blah" format="blast">
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
41 <files>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
42 <trackFile path="test-data/blastxml/blast.xml" ext="blastxml" label="BlastP, min_gap=3"/>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
43 </files>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
44
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
45 <options>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
46 <style>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
47 <className>feature</className>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
48 <description></description>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
49 <label>Description</label>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
50 <height>400px</height>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
51 </style>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
52 <blast>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
53 <parent>test-data/blastxml/merlin.gff</parent>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
54 <protein>true</protein>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
55 <min_gap>3</min_gap>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
56 </blast>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
57 <scaling>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
58 <method>score</method>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
59 <algo>blast</algo>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
60 <scales>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
61 <type>__auto__</type>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
62 </scales>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
63 <scheme>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
64 <type>opacity</type>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
65 <color>__auto__</color>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
66 </scheme>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
67 </scaling>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
68 </options>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
69 </track>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
70
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
71 <track cat="Blah" format="blast">
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
72 <files>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
73 <trackFile path="test-data/blastxml/blast-gene1.xml" ext="blastxml" label="Non protein match/matchpart"/>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
74 </files>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
75
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
76 <options>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
77 <style>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
78 <className>feature</className>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
79 <description></description>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
80 <label>Description</label>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
81 <height>400px</height>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
82 </style>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
83 <blast>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
84 <parent>test-data/blastxml/merlin.gff</parent>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
85 <min_gap>3</min_gap>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
86 </blast>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
87 <scaling>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
88 <method>ignore</method>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
89 <algo>linear</algo>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
90 <scheme>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
91 <type>opacity</type>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
92 <color>__auto__</color>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
93 </scheme>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
94 </scaling>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
95 </options>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
96 </track>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
97
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
98 <track cat="Blah" format="blast">
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
99 <files>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
100 <trackFile path="test-data/blastxml/blastn-gene1.xml" ext="blastxml" label="Non protein match/matchpart, no parent"/>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
101 </files>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
102
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
103 <options>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
104 <style>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
105 <className>feature</className>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
106 <description></description>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
107 <label>Description</label>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
108 <height>400px</height>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
109 </style>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
110 <blast>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
111 <min_gap>40</min_gap>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
112 </blast>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
113 <scaling>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
114 <method>score</method>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
115 <algo>blast</algo>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
116 <scales>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
117 <type>__auto__</type>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
118 </scales>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
119 <scheme>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
120 <type>opacity</type>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
121 <color>__auto__</color>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
122 </scheme>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
123 </scaling>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
124 </options>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
125 </track>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
126
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
127 </tracks>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents:
diff changeset
128 </root>