variability-profile-xml

Provided by
Required or used by
Description

XML

A XML-type anvi’o artifact. This artifact can be generated, used, and/or exported by anvi’o. It can also be provided by the user for anvi’o to import into its databases, process, and/or use.

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Provided by

anvi-gen-variability-network

Required or used by

There are no anvi’o tools that use or require this artifact directly, which means it is most likely an end-product for the user.

Description

An XML formatted network file that can be read and visualized by the program Gephi.

At the time of preparing this particular artifact document, An example output looked like this:

<?xml version="1.0" encoding="UTF-8"?>
<gexf xmlns:viz="http:///www.gexf.net/1.1draft/viz" xmlns="http://www.gexf.net/1.2draft" version="1.2">
<meta lastmodifieddate="2010-01-01+23:42">
    <creator>Oligotyping pipeline</creator>
</meta>
<graph type="static" defaultedgetype="undirected">

<nodes>
    <node id="FIN_0226C_014D" label="FIN_0226C_014D">
        <viz:size value="8"/>
    </node>
    <node id="FIN_0226C_030D" label="FIN_0226C_030D">
        <viz:size value="8"/>
    </node>
    <node id="FIN_0226C_090D" label="FIN_0226C_090D">
        <viz:size value="8"/>
    </node>
    <node id="FIN_0226M_000A" label="FIN_0226M_000A">
        <viz:size value="8"/>
    </node>
    <node id="FIN_0226M_000B" label="FIN_0226M_000B">
        <viz:size value="8"/>
    </node>
    (...)
</nodes>
<edges>
    <edge id="0" source="AA_1004_0" target="FIN_0226C_014D" weight="154.000000" />
    <edge id="1" source="AA_1031_0" target="FIN_0226C_014D" weight="144.000000" />
    <edge id="2" source="AA_1050_0" target="FIN_0226C_014D" weight="133.000000" />
    <edge id="3" source="AA_1250_0" target="FIN_0226C_014D" weight="50.000000" />
    <edge id="4" source="AA_1268_0" target="FIN_0226C_014D" weight="41.000000" />
    <edge id="5" source="AA_1280_0" target="FIN_0226C_014D" weight="33.000000" />
    <edge id="6" source="AA_1298_0" target="FIN_0226C_014D" weight="19.000000" />
    <edge id="7" source="AA_1299_0" target="FIN_0226C_014D" weight="19.000000" />
    <edge id="8" source="AA_1304_0" target="FIN_0226C_014D" weight="11.000000" />
    (...)
    <edge id="3709" source="GT_1013_0" target="USA_0129M_000D" weight="3.000000" />
    <edge id="3710" source="GT_1016_0" target="USA_0129M_000D" weight="11.000000" />
    <edge id="3711" source="GT_1120_0" target="USA_0129M_000D" weight="1.000000" />
    <edge id="3712" source="GT_1172_0" target="USA_0129M_000D" weight="3.000000" />
    <edge id="3713" source="GT_389_0" target="USA_0129M_000D" weight="2.000000" />
    <edge id="3714" source="GT_458_0" target="USA_0129M_000D" weight="4.000000" />
    <edge id="3715" source="GT_512_0" target="USA_0129M_000D" weight="1.000000" />
    <edge id="3716" source="GT_518_0" target="USA_0129M_000D" weight="2.000000" />
    <edge id="3717" source="GT_533_0" target="USA_0129M_000D" weight="1.000000" />
    <edge id="3718" source="GT_570_0" target="USA_0129M_000D" weight="1.000000" />
    <edge id="3719" source="GT_581_0" target="USA_0129M_000D" weight="1.000000" />
    <edge id="3720" source="GT_602_0" target="USA_0129M_000D" weight="3.000000" />
    <edge id="3721" source="GT_707_0" target="USA_0129M_000D" weight="3.000000" />
    <edge id="3722" source="GT_762_0" target="USA_0129M_000D" weight="3.000000" />
    <edge id="3723" source="GT_878_0" target="USA_0129M_000D" weight="2.000000" />
    <edge id="3724" source="GT_887_0" target="USA_0129M_000D" weight="5.000000" />
    <edge id="3725" source="GT_899_0" target="USA_0129M_000D" weight="6.000000" />
</edges>
</graph>
</gexf>

Edit this file to update this information.