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

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Uploaded v0.4 of JBrowse
author iuc
date Thu, 31 Dec 2015 13:58:43 -0500
parents
children ff11d442feed
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/blastxml/test.xml	Thu Dec 31 13:58:43 2015 -0500
@@ -0,0 +1,128 @@
+<?xml version="1.0"?>
+<root>
+    <metadata>
+        <gencode>11</gencode>
+        <genomes>
+            <genome>test-data/merlin.fa</genome>
+        </genomes>
+    </metadata>
+    <tracks>
+        <track cat="Blah" format="blast">
+            <files>
+                <trackFile path="test-data/blastxml/blast.xml" ext="blastxml" label="BlastP"/>
+            </files>
+
+            <options>
+                <style>
+                    <className>feature</className>
+                    <description></description>
+                    <label>Description</label>
+                    <height>400px</height>
+                </style>
+                <blast>
+                    <parent>test-data/blastxml/merlin.gff</parent>
+                    <protein>true</protein>
+                    <min_gap>10</min_gap>
+                </blast>
+                <scaling>
+                    <method>score</method>
+                    <algo>blast</algo>
+                    <scales>
+                        <type>__auto__</type>
+                    </scales>
+                    <scheme>
+                        <type>opacity</type>
+                        <color>__auto__</color>
+                    </scheme>
+                </scaling>
+            </options>
+        </track>
+        <track cat="Blah" format="blast">
+            <files>
+                <trackFile path="test-data/blastxml/blast.xml" ext="blastxml" label="BlastP, min_gap=3"/>
+            </files>
+
+            <options>
+                <style>
+                    <className>feature</className>
+                    <description></description>
+                    <label>Description</label>
+                    <height>400px</height>
+                </style>
+                <blast>
+                    <parent>test-data/blastxml/merlin.gff</parent>
+                    <protein>true</protein>
+                    <min_gap>3</min_gap>
+                </blast>
+                <scaling>
+                    <method>score</method>
+                    <algo>blast</algo>
+                    <scales>
+                        <type>__auto__</type>
+                    </scales>
+                    <scheme>
+                        <type>opacity</type>
+                        <color>__auto__</color>
+                    </scheme>
+                </scaling>
+            </options>
+        </track>
+
+        <track cat="Blah" format="blast">
+            <files>
+                <trackFile path="test-data/blastxml/blast-gene1.xml" ext="blastxml" label="Non protein match/matchpart"/>
+            </files>
+
+            <options>
+                <style>
+                    <className>feature</className>
+                    <description></description>
+                    <label>Description</label>
+                    <height>400px</height>
+                </style>
+                <blast>
+                    <parent>test-data/blastxml/merlin.gff</parent>
+                    <min_gap>3</min_gap>
+                </blast>
+                <scaling>
+                    <method>ignore</method>
+                    <algo>linear</algo>
+                    <scheme>
+                        <type>opacity</type>
+                        <color>__auto__</color>
+                    </scheme>
+                </scaling>
+            </options>
+        </track>
+
+        <track cat="Blah" format="blast">
+            <files>
+                <trackFile path="test-data/blastxml/blastn-gene1.xml" ext="blastxml" label="Non protein match/matchpart, no parent"/>
+            </files>
+
+            <options>
+                <style>
+                    <className>feature</className>
+                    <description></description>
+                    <label>Description</label>
+                    <height>400px</height>
+                </style>
+                <blast>
+                    <min_gap>40</min_gap>
+                </blast>
+                <scaling>
+                    <method>score</method>
+                    <algo>blast</algo>
+                    <scales>
+                        <type>__auto__</type>
+                    </scales>
+                    <scheme>
+                        <type>opacity</type>
+                        <color>__auto__</color>
+                    </scheme>
+                </scaling>
+            </options>
+        </track>
+
+    </tracks>
+</root>