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Adding basic unit tests for NeXML parser using example files from nexml.org.
This commit is contained in:
bendmorris
committed by
Eric Talevich
Eric Talevich
parent
5390a48460
commit
02e7e0ac91
532
Tests/NeXML/characters.xml
Normal file
532
Tests/NeXML/characters.xml
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@ -0,0 +1,532 @@
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<?xml version="1.0" encoding="ISO-8859-1"?>
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<!--
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This file shows encodings of character state data.
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-->
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<!--
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For more discussion of the structure of the root element,
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refer to 'taxa.xml'
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-->
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<nex:nexml
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version="0.9"
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xml:base="http://example.org/"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://www.nexml.org/2009 ../xsd/nexml.xsd"
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xmlns:nex="http://www.nexml.org/2009"
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xmlns="http://www.nexml.org/2009">
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<!--
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For more discussion of the structure of the taxa
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element, refer to 'taxa.xml'
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-->
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<otus id="taxa1" label="Primary taxa block">
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<otu id="t1" label="Homo sapiens"/>
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<otu id="t2" label="Pan paniscus"/>
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<otu id="t3" label="Pan troglodytes"/>
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<otu id="t4" label="Gorilla gorilla"/>
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<otu id="t5" label="Pongo pygmaeus"/>
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</otus>
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<!--
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This characters block encodes restriction site data, i.e.
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presence (1) / absence (0) observations. Because the states
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that can occur - and what they mean - are known, there is no
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'format' element to define states (see below for examples of
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that). In this example, restriction site data is encoded
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as a sequence of characters (rather than individual cells),
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hence we use the subclass xsi:type="RestrictionSeqs".
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All characters blocks must have an id attribute and a
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reference to a taxa block that precedes it. In addition,
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it may have the same additional attributes (label, xml:base,
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xml:lang, xml:id, xlink:href and class) as the taxa element.
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-->
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<characters otus="taxa1" id="m1" xsi:type="nex:RestrictionSeqs" label="Restriction site sequences">
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<format>
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<states id="RestrictionSiteStateSet">
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<state id="Absent" symbol="0"/>
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<state id="Present" symbol="1"/>
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</states>
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<char id="Site1" states="RestrictionSiteStateSet"/>
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<char id="Site2" states="RestrictionSiteStateSet"/>
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<char id="Site3" states="RestrictionSiteStateSet"/>
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<char id="Site4" states="RestrictionSiteStateSet"/>
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</format>
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<matrix>
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<!--
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The matrix element is a container for row elements.
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-->
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<!--
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Each row element must have an id and a reference
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to a taxon element that precedes it.
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-->
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<row otu="t1" id="RestrictionSiteRow1">
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<!--
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Because this characters block is an instance
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of the subclass RestrictionSeqs it contains
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'seq' elements with 1's and 0's.
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-->
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<seq>0101</seq>
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</row>
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<row otu="t2" id="RestrictionSiteRow2">
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<seq>0101</seq>
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</row>
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<row otu="t3" id="RestrictionSiteRow3">
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<seq>0101</seq>
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</row>
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<row otu="t4" id="RestrictionSiteRow4">
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<seq>0101</seq>
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</row>
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<row otu="t5" id="RestrictionSiteRow5">
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<seq>0101</seq>
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</row>
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</matrix>
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</characters>
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<!--
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This characters block encodes 'standard' categorical characters,
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marked up granularly, as cells.
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-->
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<characters otus="taxa1" id="m2" xsi:type="nex:StandardCells" label="Categorical characters">
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<!--
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Because categorical characters in instances of this subclass
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don't have a priori known numbers of states, they must be
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defined using the 'format' element.
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-->
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<format>
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<!--
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The first elements inside a format element are stateset
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definitions. In this example, there is a set of four
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states, each tagged with an id. The symbol attribute is
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a shorthand token that would be used when serializing to
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NEXUS, for example.
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-->
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<states id="StandardCategoricalStateSet1">
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<state id="StandardCategoricalState1" symbol="1"/>
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<state id="StandardCategoricalState2" symbol="2"/>
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<state id="StandardCategoricalState3" symbol="3"/>
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<polymorphic_state_set symbol="4" id="StandardCategoricalState4">
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<member state="StandardCategoricalState2"/>
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<member state="StandardCategoricalState3"/>
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</polymorphic_state_set>
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<uncertain_state_set symbol="5" id="StandardCategoricalState5">
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<member state="StandardCategoricalState1"/>
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<member state="StandardCategoricalState2"/>
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</uncertain_state_set>
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</states>
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<!--
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The matrix in this example contains two columns, both
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referring to the same stateset - and so cells in both
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columns can occupy one of four states.
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-->
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<char states="StandardCategoricalStateSet1" id="StandardCharacter1"/>
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<char states="StandardCategoricalStateSet1" id="StandardCharacter2"/>
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</format>
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<!--
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In this subclass, the matrix contains rows consisting of
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individual cells.
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-->
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<matrix>
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<row id="StandardCategoricalStateCellsRow1" otu="t1">
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<!--
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Each cell must contain a reference to the column
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it belongs to, and to a state allowed within that
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column.
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-->
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<cell char="StandardCharacter1" state="StandardCategoricalState1"/>
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<cell char="StandardCharacter2" state="StandardCategoricalState2"/>
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</row>
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<row id="StandardCategoricalStateCellsRow2" otu="t2">
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<cell char="StandardCharacter1" state="StandardCategoricalState2"/>
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<cell char="StandardCharacter2" state="StandardCategoricalState2"/>
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</row>
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<row id="StandardCategoricalStateCellsRow3" otu="t3">
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<cell char="StandardCharacter1" state="StandardCategoricalState3"/>
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<cell char="StandardCharacter2" state="StandardCategoricalState4"/>
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</row>
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<row id="StandardCategoricalStateCellsRow4" otu="t4">
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<cell char="StandardCharacter1" state="StandardCategoricalState2"/>
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<cell char="StandardCharacter2" state="StandardCategoricalState3"/>
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</row>
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<row id="StandardCategoricalStateCellsRow5" otu="t5">
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<cell char="StandardCharacter1" state="StandardCategoricalState4"/>
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<cell char="StandardCharacter2" state="StandardCategoricalState1"/>
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</row>
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</matrix>
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</characters>
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<!--
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This example is a characters block for continuous characters, marked
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up as individual cells.
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-->
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<characters otus="taxa1" id="m3" xsi:type="nex:ContinuousCells" label="Continuous characters">
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<format>
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<!--
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Because in this subclass, characters are marked up granularly -
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as cells - we must define the columns these cells belong to.
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Because this is continuous data, we don't (can't) define the
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states cells in these columns may occupy, hence there are no
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'states' elements in this subclass.
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-->
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<char id="ContinuousCharacter1" label="this is character 1"/>
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<char id="ContinuousCharacter2"/>
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<char id="ContinuousCharacter3"/>
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<char id="ContinuousCharacter4"/>
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<char id="ContinuousCharacter5"/>
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</format>
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<matrix>
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<row id="ContinuousCellsRow1" otu="t1">
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<!--
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In this subclass, the 'state' attribute holds the raw
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value of the cell (i.e. a floating point number), not
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a reference to a state defined previously.
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-->
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<cell char="ContinuousCharacter1" state="-1.545414144070023"/>
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<cell char="ContinuousCharacter2" state="-2.3905621575431044"/>
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<cell char="ContinuousCharacter3" state="-2.9610221833467265"/>
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<cell char="ContinuousCharacter4" state="0.7868662069161243"/>
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<cell char="ContinuousCharacter5" state="0.22968509237534918"/>
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</row>
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<row id="ContinuousCellsRow2" otu="t2">
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<cell char="ContinuousCharacter1" state="-1.6259836379710066"/>
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<cell char="ContinuousCharacter2" state="3.649352410850134"/>
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<cell char="ContinuousCharacter3" state="1.778885099660406"/>
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<cell char="ContinuousCharacter4" state="-1.2580877968480846"/>
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<cell char="ContinuousCharacter5" state="0.22335354995610862"/>
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</row>
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<row id="ContinuousCellsRow3" otu="t3">
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<cell char="ContinuousCharacter1" state="-1.5798979984134964"/>
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<cell char="ContinuousCharacter2" state="2.9548251411133157"/>
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<cell char="ContinuousCharacter3" state="1.522005675256233"/>
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<cell char="ContinuousCharacter4" state="-0.8642016921755289"/>
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<cell char="ContinuousCharacter5" state="-0.938129801832388"/>
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</row>
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<row id="ContinuousCellsRow4" otu="t4">
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<cell char="ContinuousCharacter1" state="2.7436692306788086"/>
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<cell char="ContinuousCharacter2" state="-0.7151148143399818"/>
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<cell char="ContinuousCharacter3" state="4.592207937774776"/>
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<cell char="ContinuousCharacter4" state="-0.6898841440534845"/>
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<cell char="ContinuousCharacter5" state="0.5769509574453064"/>
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</row>
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<row id="ContinuousCellsRow5" otu="t5">
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<cell char="ContinuousCharacter1" state="3.1060827493657683"/>
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<cell char="ContinuousCharacter2" state="-1.0453787389160105"/>
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<cell char="ContinuousCharacter3" state="2.67416332763427"/>
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<cell char="ContinuousCharacter4" state="-1.4045634106692808"/>
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<cell char="ContinuousCharacter5" state="0.019890469925520196"/>
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</row>
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</matrix>
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</characters>
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<!--
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This subclass encodes DNA as sequences (not cells). Like the restriction
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site data block shown above, the states are known (being IUPAC single
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character nucleotide symbols), hence there is no 'format' element. In
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addition to the IUPAC symbols, '-' is used for gaps, '?' is used for
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missing. Spaces are allowed (so that long lines can be broken up, some
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parsers might otherwise complain) but have no meaning.
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-->
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<characters otus="taxa1" id="characters3" xsi:type="nex:DnaSeqs" label="DNA sequences">
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<format>
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<states id="IUPACDNAStateSet1">
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<state id="NucA" symbol="A" />
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<state id="NucC" symbol="C" />
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<state id="NucG" symbol="G" />
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<state id="NucT" symbol="T" />
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<uncertain_state_set id="SymK" symbol="K">
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<member state="NucG" />
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<member state="NucT" />
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</uncertain_state_set>
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<uncertain_state_set id="SymM" symbol="M">
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<member state="NucA" />
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<member state="NucC" />
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</uncertain_state_set>
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<uncertain_state_set id="SymR" symbol="R">
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<member state="NucA" />
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<member state="NucG" />
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</uncertain_state_set>
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<uncertain_state_set id="SymS" symbol="S">
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<member state="NucC" />
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<member state="NucG" />
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</uncertain_state_set>
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<uncertain_state_set id="SymW" symbol="W">
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<member state="NucA" />
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<member state="NucT" />
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</uncertain_state_set>
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<uncertain_state_set id="SymY" symbol="Y">
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<member state="NucC" />
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<member state="NucT" />
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</uncertain_state_set>
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<uncertain_state_set id="SymB" symbol="B">
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<member state="NucC" />
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<member state="NucG" />
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<member state="NucT" />
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</uncertain_state_set>
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<uncertain_state_set id="SymD" symbol="D">
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<member state="NucA" />
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<member state="NucG" />
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<member state="NucT" />
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</uncertain_state_set>
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<uncertain_state_set id="SymH" symbol="H">
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<member state="NucA" />
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<member state="NucC" />
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<member state="NucT" />
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</uncertain_state_set>
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<uncertain_state_set id="SymV" symbol="V">
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<member state="NucA" />
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<member state="NucC" />
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<member state="NucG" />
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</uncertain_state_set>
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<uncertain_state_set id="SymN" symbol="N">
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<member state="NucA" />
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<member state="NucC" />
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<member state="NucG" />
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<member state="NucT" />
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</uncertain_state_set>
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<uncertain_state_set id="SymX" symbol="X">
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<member state="NucA" />
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<member state="NucC" />
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<member state="NucG" />
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<member state="NucT" />
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</uncertain_state_set>
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<uncertain_state_set id="SymGap" symbol="-" />
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<uncertain_state_set id="SymMiss" symbol="?">
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<member state="NucA" />
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<member state="NucC" />
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<member state="NucG" />
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<member state="NucT" />
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<member state="SymK" />
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<member state="SymM" />
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<member state="SymR" />
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<member state="SymS" />
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<member state="SymW" />
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<member state="SymY" />
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<member state="SymB" />
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<member state="SymD" />
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<member state="SymH" />
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<member state="SymV" />
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<member state="SymN" />
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<member state="SymX" />
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<member state="SymGap" />
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</uncertain_state_set>
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</states>
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<char id="ResidueCol1" states="IUPACDNAStateSet1" />
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<char id="ResidueCol2" states="IUPACDNAStateSet1" />
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<char id="ResidueCol3" states="IUPACDNAStateSet1" />
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<char id="ResidueCol4" states="IUPACDNAStateSet1" />
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<char id="ResidueCol5" states="IUPACDNAStateSet1" />
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<char id="ResidueCol6" states="IUPACDNAStateSet1" />
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<char id="ResidueCol7" states="IUPACDNAStateSet1" />
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<char id="ResidueCol8" states="IUPACDNAStateSet1" />
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<char id="ResidueCol9" states="IUPACDNAStateSet1" />
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<char id="ResidueCol10" states="IUPACDNAStateSet1" />
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<char id="ResidueCol11" states="IUPACDNAStateSet1" />
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<char id="ResidueCol12" states="IUPACDNAStateSet1" />
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<char id="ResidueCol13" states="IUPACDNAStateSet1" />
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<char id="ResidueCol14" states="IUPACDNAStateSet1" />
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<char id="ResidueCol15" states="IUPACDNAStateSet1" />
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<char id="ResidueCol16" states="IUPACDNAStateSet1" />
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</format>
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<matrix>
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<row otu="t1" id="DNASequence1"><seq>A C G C T C G C A T C G C A T C</seq></row>
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<row otu="t2" id="DNASequence2"><seq>A C G C T C G C A T C G C A T C</seq></row>
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<row otu="t3" id="DNASequence3"><seq>A C G C T C G C A T C G C A T C</seq></row>
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</matrix>
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</characters>
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<!--
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RNA only differs from the previous example by using U instead of T
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-->
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<characters otus="taxa1" id="rnaseqs4" xsi:type="nex:RnaSeqs" label="RNA sequences">
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<format>
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<states id="rnastates">
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<state id="rna1" symbol="A"/>
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<state id="rna2" symbol="C"/>
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<state id="rna3" symbol="G"/>
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<state id="rna4" symbol="U"/>
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<uncertain_state_set id="rna5" symbol="K">
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<member state="rna3"/>
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<member state="rna4"/>
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</uncertain_state_set>
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<uncertain_state_set id="rna6" symbol="M">
|
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<member state="rna1"/>
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<member state="rna2"/>
|
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</uncertain_state_set>
|
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<uncertain_state_set id="rna7" symbol="R">
|
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<member state="rna1"/>
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<member state="rna3"/>
|
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</uncertain_state_set>
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<uncertain_state_set id="rna8" symbol="S">
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<member state="rna2"/>
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<member state="rna3"/>
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</uncertain_state_set>
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<uncertain_state_set id="rna9" symbol="W">
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<member state="rna1"/>
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<member state="rna4"/>
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</uncertain_state_set>
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<uncertain_state_set id="rna10" symbol="Y">
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<member state="rna2"/>
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<member state="rna4"/>
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</uncertain_state_set>
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<uncertain_state_set id="rna11" symbol="B">
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<member state="rna2"/>
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<member state="rna3"/>
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<member state="rna4"/>
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</uncertain_state_set>
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<uncertain_state_set id="rna12" symbol="D">
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<member state="rna1"/>
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<member state="rna3"/>
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<member state="rna4"/>
|
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</uncertain_state_set>
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<uncertain_state_set id="rna13" symbol="H">
|
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<member state="rna1"/>
|
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<member state="rna2"/>
|
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<member state="rna4"/>
|
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</uncertain_state_set>
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<uncertain_state_set id="rna14" symbol="V">
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<member state="rna1"/>
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<member state="rna2"/>
|
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<member state="rna3"/>
|
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</uncertain_state_set>
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<uncertain_state_set id="rna15" symbol="N">
|
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<member state="rna3"/>
|
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<member state="rna1"/>
|
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<member state="rna4"/>
|
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<member state="rna2"/>
|
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</uncertain_state_set>
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<uncertain_state_set id="rna16" symbol="X">
|
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<member state="rna3"/>
|
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<member state="rna1"/>
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<member state="rna4"/>
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<member state="rna2"/>
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</uncertain_state_set>
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<uncertain_state_set id="rna17" symbol="-"/>
|
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<uncertain_state_set id="rna18" symbol="?">
|
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<member state="rna1"/>
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<member state="rna2"/>
|
||||
<member state="rna3"/>
|
||||
<member state="rna4"/>
|
||||
<member state="rna5"/>
|
||||
<member state="rna6"/>
|
||||
<member state="rna7"/>
|
||||
<member state="rna8"/>
|
||||
<member state="rna9"/>
|
||||
<member state="rna10"/>
|
||||
<member state="rna11"/>
|
||||
<member state="rna12"/>
|
||||
<member state="rna13"/>
|
||||
<member state="rna14"/>
|
||||
<member state="rna15"/>
|
||||
<member state="rna16"/>
|
||||
<member state="rna17"/>
|
||||
</uncertain_state_set>
|
||||
</states>
|
||||
<char id="rnachar1" states="rnastates"/>
|
||||
<char id="rnachar2" states="rnastates"/>
|
||||
<char id="rnachar3" states="rnastates"/>
|
||||
<char id="rnachar4" states="rnastates"/>
|
||||
<char id="rnachar5" states="rnastates"/>
|
||||
<char id="rnachar6" states="rnastates"/>
|
||||
<char id="rnachar7" states="rnastates"/>
|
||||
<char id="rnachar8" states="rnastates"/>
|
||||
<char id="rnachar9" states="rnastates"/>
|
||||
<char id="rnachar10" states="rnastates"/>
|
||||
<char id="rnachar11" states="rnastates"/>
|
||||
<char id="rnachar12" states="rnastates"/>
|
||||
<char id="rnachar13" states="rnastates"/>
|
||||
<char id="rnachar14" states="rnastates"/>
|
||||
<char id="rnachar15" states="rnastates"/>
|
||||
<char id="rnachar16" states="rnastates"/>
|
||||
<char id="rnachar17" states="rnastates"/>
|
||||
<char id="rnachar18" states="rnastates"/>
|
||||
<char id="rnachar19" states="rnastates"/>
|
||||
<char id="rnachar20" states="rnastates"/>
|
||||
</format>
|
||||
<matrix>
|
||||
<row otu="t1" id="rnarow1">
|
||||
<seq>ACGCUCGCAUCGCAUC</seq>
|
||||
</row>
|
||||
<row otu="t2" id="rnarow2">
|
||||
<seq>ACGCUCGCAUCGCAUC</seq>
|
||||
</row>
|
||||
<row otu="t3" id="rnarow3">
|
||||
<seq>ACGCUCGCAUCGCAUC</seq>
|
||||
</row>
|
||||
</matrix>
|
||||
</characters>
|
||||
<!--
|
||||
A more compact example of encoding of continuous characters as raw sequences.
|
||||
-->
|
||||
<characters otus="taxa1" id="contchars5" xsi:type="nex:ContinuousSeqs" label="Continuous sequences">
|
||||
<format>
|
||||
<char id="contchar1"/>
|
||||
<char id="contchar2"/>
|
||||
<char id="contchar3"/>
|
||||
<char id="contchar4"/>
|
||||
<char id="contchar5"/>
|
||||
</format>
|
||||
<matrix>
|
||||
<row id="controw1" otu="t1">
|
||||
<seq>-1.545414144070023 -2.3905621575431044 -2.9610221833467265 0.7868662069161243 0.22968509237534918</seq>
|
||||
</row>
|
||||
<row id="controw2" otu="t2">
|
||||
<seq>-1.6259836379710066 3.649352410850134 1.778885099660406 -1.2580877968480846 0.22335354995610862</seq>
|
||||
</row>
|
||||
<row id="controw3" otu="t3">
|
||||
<seq>-1.5798979984134964 2.9548251411133157 1.522005675256233 -0.8642016921755289 -0.938129801832388</seq>
|
||||
</row>
|
||||
<row id="controw4" otu="t4">
|
||||
<seq>2.7436692306788086 -0.7151148143399818 4.592207937774776 -0.6898841440534845 0.5769509574453064</seq>
|
||||
</row>
|
||||
<row id="controw5" otu="t5">
|
||||
<seq>3.1060827493657683 -1.0453787389160105 2.67416332763427 -1.4045634106692808 0.019890469925520196</seq>
|
||||
</row>
|
||||
</matrix>
|
||||
</characters>
|
||||
<!--
|
||||
A more compact example of encoding of standard data. Note that the symbols used here
|
||||
are integers (also above 9) and so characters must be space-separated. The symbols used
|
||||
here are the same as the symbol attributes used in characters block m2, earlier.
|
||||
-->
|
||||
<characters otus="taxa1" id="standardchars6" xsi:type="nex:StandardSeqs" label="Standard sequences">
|
||||
<format>
|
||||
<!--
|
||||
The first elements inside a format element are stateset
|
||||
definitions. In this example, there is a set of four
|
||||
states, each tagged with an id. The symbol attribute is
|
||||
a shorthand token.
|
||||
-->
|
||||
<states id="standardstateset1">
|
||||
<state id="standardstates1" symbol="1"/>
|
||||
<state id="standardstates2" symbol="2"/>
|
||||
<state id="standardstates3" symbol="3"/>
|
||||
<polymorphic_state_set symbol="4" id="standardstates4">
|
||||
<member state="standardstates1"/>
|
||||
<member state="standardstates2"/>
|
||||
</polymorphic_state_set>
|
||||
<uncertain_state_set symbol="5" id="standardstates5">
|
||||
<member state="standardstates3"/>
|
||||
<member state="standardstates1"/>
|
||||
</uncertain_state_set>
|
||||
</states>
|
||||
<!--
|
||||
The matrix in this example contains two columns, both
|
||||
referring to the same stateset - and so cells in both
|
||||
columns can occupy one of four states.
|
||||
-->
|
||||
<char states="standardstateset1" id="standardc1"/>
|
||||
<char states="standardstateset1" id="standardc2"/>
|
||||
</format>
|
||||
<matrix>
|
||||
<row id="standardr1" otu="t1">
|
||||
<seq>1 2</seq>
|
||||
</row>
|
||||
<row id="standardr2" otu="t2">
|
||||
<seq>2 2</seq>
|
||||
</row>
|
||||
<row id="standardr3" otu="t3">
|
||||
<seq>3 4</seq>
|
||||
</row>
|
||||
<row id="standardr4" otu="t4">
|
||||
<seq>2 3</seq>
|
||||
</row>
|
||||
<row id="standardr5" otu="t5">
|
||||
<seq>4 1</seq>
|
||||
</row>
|
||||
</matrix>
|
||||
</characters>
|
||||
</nex:nexml>
|
||||
38
Tests/NeXML/edgelabels.xml
Normal file
38
Tests/NeXML/edgelabels.xml
Normal file
@ -0,0 +1,38 @@
|
||||
<?xml version="1.0" encoding="ISO-8859-1"?>
|
||||
<nex:nexml
|
||||
version="0.9"
|
||||
xml:base="http://example.org/"
|
||||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||
xsi:schemaLocation="http://www.nexml.org/2009 http://www.nexml.org/2009/nexml.xsd"
|
||||
xmlns:nex="http://www.nexml.org/2009"
|
||||
xmlns:xsd="http://www.w3.org/2001/XMLSchema"
|
||||
xmlns="http://www.nexml.org/2009">
|
||||
<otus id="tax1" label="RootTaxaBlock">
|
||||
<otu id="t1"/>
|
||||
<otu id="t2"/>
|
||||
<otu id="t3"/>
|
||||
<otu id="t4"/>
|
||||
<otu id="t5"/>
|
||||
</otus>
|
||||
<trees otus="tax1" id="Trees" label="TreesBlockFromXML">
|
||||
<tree id="tree1" xsi:type="nex:FloatTree" label="tree1">
|
||||
<node id="n1" label="n1" root="true"/>
|
||||
<node id="n2" label="n2" otu="t1"/>
|
||||
<node id="n3" label="n3"/>
|
||||
<node id="n4" label="n4"/>
|
||||
<node id="n5" label="n5" otu="t3"/>
|
||||
<node id="n6" label="n6" otu="t2"/>
|
||||
<node id="n7" label="n7"/>
|
||||
<node id="n8" label="n8" otu="t5"/>
|
||||
<node id="n9" label="n9" otu="t4"/>
|
||||
<edge source="n1" target="n3" id="e1" label="e1"/>
|
||||
<edge source="n1" target="n2" id="e2" label="e2"/>
|
||||
<edge source="n3" target="n4" id="e3" label="e3"/>
|
||||
<edge source="n3" target="n7" id="e4" label="e4"/>
|
||||
<edge source="n4" target="n5" id="e5" label="e5"/>
|
||||
<edge source="n4" target="n6" id="e6" label="e6"/>
|
||||
<edge source="n7" target="n8" id="e7" label="e7"/>
|
||||
<edge source="n7" target="n9" id="e8" label="e8"/>
|
||||
</tree>
|
||||
</trees>
|
||||
</nex:nexml>
|
||||
49
Tests/NeXML/meta_taxa.xml
Normal file
49
Tests/NeXML/meta_taxa.xml
Normal file
@ -0,0 +1,49 @@
|
||||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<nex:nexml
|
||||
generator="Bio::Phylo::Project v.0.17_RC9_1175"
|
||||
version="0.9"
|
||||
xml:base="http://example.org/"
|
||||
xmlns="http://www.nexml.org/2009"
|
||||
xmlns:nex="http://www.nexml.org/2009"
|
||||
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
|
||||
xmlns:xml="http://www.w3.org/XML/1998/namespace"
|
||||
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
|
||||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||
xmlns:cdao="http://www.evolutionaryontology.org/cdao/1.0/cdao.owl#"
|
||||
xsi:schemaLocation="http://www.nexml.org/2009 ../xsd/nexml.xsd">
|
||||
<otus
|
||||
id="aabef8df4-6968-4d97-961d-b28210c0b318"
|
||||
about="#aabef8df4-6968-4d97-961d-b28210c0b318"
|
||||
label="Taxa"
|
||||
xmlns:dwc="http://I-GUESS-THIS-SHOULD-BE-DARWINCORE.org#">
|
||||
<meta
|
||||
href="http://purl.org/obo/owl/TTO#TTO_1030115"
|
||||
id="ad37ab715-8dc6-4959-9b20-c58d5edaef29"
|
||||
xsi:type="nex:ResourceMeta"
|
||||
rel="cdao:has_External_Reference"/>
|
||||
<meta
|
||||
id="EDA14D9B-9669-48F1-A79A-761DAA82038B"
|
||||
about="#EDA14D9B-9669-48F1-A79A-761DAA82038B"
|
||||
xsi:type="nex:ResourceMeta"
|
||||
rel="cdao:hasSpecimen">
|
||||
<meta
|
||||
id="C9F5CAA3-421B-4830-8DC5-686FD75EB9F3"
|
||||
xsi:type="nex:ResourceMeta"
|
||||
rel="dwc:collectionID"
|
||||
href="http://purl.org/obo/owl/COLLECTION#COLLECTION_0000194"/>
|
||||
<meta
|
||||
id="C3E89AAC-AFE3-4225-869C-A2380B6EF83E"
|
||||
datatype="xsd:string"
|
||||
xsi:type="nex:LiteralMeta"
|
||||
property="dwc:catalogNumber"
|
||||
content="12345"/>
|
||||
</meta>
|
||||
<otu
|
||||
xmlns:cdao="http://evolutionaryontology.org#"
|
||||
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
|
||||
about="#aaa0ec8a9-7b38-411f-9c4d-f4a47bcffac3"
|
||||
id="aaa0ec8a9-7b38-411f-9c4d-f4a47bcffac3"
|
||||
label="Nannostomus unifasciatus">
|
||||
</otu>
|
||||
</otus>
|
||||
</nex:nexml>
|
||||
27
Tests/NeXML/meta_types.xml
Normal file
27
Tests/NeXML/meta_types.xml
Normal file
@ -0,0 +1,27 @@
|
||||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<nex:nexml
|
||||
generator="Bio::Phylo::Project v.0.17_RC9_1175"
|
||||
version="0.9"
|
||||
xml:base="http://example.org/base/"
|
||||
xmlns="http://www.nexml.org/2009"
|
||||
xmlns:kt="http://example.org/knownTypes#"
|
||||
xmlns:nex="http://www.nexml.org/2009"
|
||||
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
|
||||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||
xsi:schemaLocation="http://www.nexml.org/2009 ../xsd/nexml.xsd">
|
||||
<otus about="#otus1" id="otus1">
|
||||
<otu about="#otu1" id="otu1">
|
||||
<meta href="http://example.org" id="meta12" rel="kt:hasURL" xsi:type="nex:ResourceMeta"/>
|
||||
<meta content="bar" datatype="xsd:string" id="meta11" property="kt:hasString" xsi:type="nex:LiteralMeta"/>
|
||||
<meta content="5" datatype="xsd:short" id="meta10" property="kt:hasShort" xsi:type="nex:LiteralMeta"/>
|
||||
<meta content="10" datatype="xsd:long" id="meta9" property="kt:hasLong" xsi:type="nex:LiteralMeta"/>
|
||||
<meta content="1.6" datatype="xsd:float" id="meta8" property="kt:hasFloat" xsi:type="nex:LiteralMeta"/>
|
||||
<meta content="1.5" datatype="xsd:double" id="meta7" property="kt:hasDouble" xsi:type="nex:LiteralMeta"/>
|
||||
<meta content="foo" datatype="xsd:QName" id="meta6" property="kt:hasQName" xsi:type="nex:LiteralMeta"/>
|
||||
<meta content="1" datatype="xsd:byte" id="meta5" property="kt:hasByte" xsi:type="nex:LiteralMeta"/>
|
||||
<meta content="true" datatype="xsd:boolean" id="meta4" property="kt:hasBoolean" xsi:type="nex:LiteralMeta"/>
|
||||
<meta content="1" datatype="xsd:integer" id="meta3" property="kt:hasBigInteger" xsi:type="nex:LiteralMeta"/>
|
||||
<meta content="0.1" datatype="xsd:decimal" id="meta2" property="kt:hasBigDecimal" xsi:type="nex:LiteralMeta"/>
|
||||
</otu>
|
||||
</otus>
|
||||
</nex:nexml>
|
||||
8
Tests/NeXML/nexml.xml
Normal file
8
Tests/NeXML/nexml.xml
Normal file
@ -0,0 +1,8 @@
|
||||
<?xml version="1.0" encoding="ISO-8859-1"?>
|
||||
<nex:nexml
|
||||
version="0.9"
|
||||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||
xsi:schemaLocation="http://www.nexml.org/2009 ../xsd/nexml.xsd"
|
||||
xmlns:xi="http://www.w3.org/2003/XInclude"
|
||||
xmlns:nex="http://www.nexml.org/2009"
|
||||
xmlns="http://www.nexml.org/2009"/>
|
||||
45
Tests/NeXML/phenoscape.xml
Normal file
45
Tests/NeXML/phenoscape.xml
Normal file
@ -0,0 +1,45 @@
|
||||
<nex:nexml
|
||||
generator="Bio::Phylo::Project v.0.17_RC9_1175"
|
||||
version="0.9"
|
||||
xml:base="http://example.org/"
|
||||
xmlns="http://www.nexml.org/2009"
|
||||
xmlns:nex="http://www.nexml.org/2009"
|
||||
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
|
||||
xmlns:xml="http://www.w3.org/XML/1998/namespace"
|
||||
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
|
||||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||
xmlns:cdao="http://www.evolutionaryontology.org/cdao/1.0/cdao.owl#"
|
||||
xsi:schemaLocation="http://www.nexml.org/2009 ../xsd/nexml.xsd">
|
||||
<otus
|
||||
id="aabef8df4-6968-4d97-961d-b28210c0b318" label="Taxa">
|
||||
<otu
|
||||
xmlns:cdao="http://evolutionaryontology.org#"
|
||||
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
|
||||
about="#aaa0ec8a9-7b38-411f-9c4d-f4a47bcffac3"
|
||||
id="aaa0ec8a9-7b38-411f-9c4d-f4a47bcffac3"
|
||||
label="Nannostomus unifasciatus"
|
||||
xmlns:dwc="http://rs.tdwg.org/dwc/terms/">
|
||||
<meta
|
||||
href="http://purl.org/obo/owl/TTO#TTO_1030115"
|
||||
id="ad37ab715-8dc6-4959-9b20-c58d5edaef29"
|
||||
xsi:type="nex:ResourceMeta"
|
||||
rel="cdao:has_External_Reference"/>
|
||||
<meta
|
||||
id="EDA14D9B-9669-48F1-A79A-761DAA82038B"
|
||||
xsi:type="nex:ResourceMeta"
|
||||
rel="cdao:hasSpecimen">
|
||||
<meta
|
||||
id="C9F5CAA3-421B-4830-8DC5-686FD75EB9F3"
|
||||
xsi:type="nex:ResourceMeta"
|
||||
rel="dwc:collectionID"
|
||||
href="http://purl.org/obo/owl/COLLECTION#COLLECTION_0000194"/>
|
||||
<meta
|
||||
id="C3E89AAC-AFE3-4225-869C-A2380B6EF83E"
|
||||
datatype="xsd:string"
|
||||
xsi:type="nex:LiteralMeta"
|
||||
property="dwc:catalogNumber"
|
||||
content="12345"/>
|
||||
</meta>
|
||||
</otu>
|
||||
</otus>
|
||||
</nex:nexml>
|
||||
36
Tests/NeXML/sets.xml
Normal file
36
Tests/NeXML/sets.xml
Normal file
@ -0,0 +1,36 @@
|
||||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<nex:nexml
|
||||
version="0.9"
|
||||
xml:base="http://example.org/"
|
||||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||
generator="handmade"
|
||||
xmlns:nex="http://www.nexml.org/2009"
|
||||
xmlns="http://www.nexml.org/2009"
|
||||
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
|
||||
xsi:schemaLocation="http://www.nexml.org/2009 ../xsd/nexml.xsd">
|
||||
<otus
|
||||
id="taxa1"
|
||||
label="My taxa block">
|
||||
<otu id="t1"/>
|
||||
<otu id="t2"/>
|
||||
<otu id="t3"/>
|
||||
<otu id="t4"/>
|
||||
<otu id="t5"/>
|
||||
<set otu="t1 t2" id="set1" about="#set1">
|
||||
<meta id="m1" xsi:type="nex:LiteralMeta" content="1" datatype="xsd:integer" xmlns:foo="http://example.org/foo#" property="foo:hasInt"/>
|
||||
</set>
|
||||
</otus>
|
||||
<trees otus="taxa1" id="trees1">
|
||||
<tree xsi:type="nex:IntTree" id="tree1">
|
||||
<node id="n1"/>
|
||||
<node id="n2"/>
|
||||
<node id="n3"/>
|
||||
<rootedge target="n1" id="root"/>
|
||||
<edge source="n1" target="n2" id="e1"/>
|
||||
<edge source="n1" target="n3" id="e2"/>
|
||||
<set edge="e1" rootedge="root" node="n1" id="set2"/>
|
||||
</tree>
|
||||
<set tree="tree1" network="tree1" id="set3"/>
|
||||
</trees>
|
||||
</nex:nexml>
|
||||
|
||||
83
Tests/NeXML/taxa.xml
Normal file
83
Tests/NeXML/taxa.xml
Normal file
@ -0,0 +1,83 @@
|
||||
<?xml version="1.0" encoding="ISO-8859-1"?>
|
||||
<!--
|
||||
This file is an example of a simple taxa block.
|
||||
-->
|
||||
<!--
|
||||
The nexml root element below is structured as follows:
|
||||
* there is a required version attribute. Additions where
|
||||
the 'core' remains backward compatible are identified
|
||||
by decimal increases (1.1, 1.2, etc.). Changes to the
|
||||
core standard are identified by integer increases (2.0,
|
||||
3.0, etc.). The former is somewhat likely to happen in
|
||||
practice, the latter hopefully isn't.
|
||||
|
||||
* In some places in instance documents, snippets of schema
|
||||
language code are necessary, for example to specify
|
||||
concrete subclasses. Such snippets are bound to the
|
||||
http://www.w3.org/2001/XMLSchema-instance namespace, and
|
||||
by convention identified by the 'xsi' prefix.
|
||||
http://en.wikipedia.org/wiki/Xsd
|
||||
|
||||
* to facilitate validation, the location of the schema is
|
||||
specified in the root element. Such a specification is
|
||||
done using the schema language snippet xsi:schemaLocation
|
||||
|
||||
* by convention, root elements of nexml fragments are
|
||||
pre-fixed with 'nex', which is bound to the namespace
|
||||
http://www.nexml.org/1.0
|
||||
|
||||
* the optional 'generator' attribute can be used to specify
|
||||
which program wrote out the file.
|
||||
|
||||
* other xml namespaces (i.e. attributes with the 'xmlns'
|
||||
prefix) can be specified here, in case they're used
|
||||
in child elements. For example, the xlink namespace
|
||||
is used for links ('href' attributes, as in html), so
|
||||
that child elements may contain links to other resources.
|
||||
http://en.wikipedia.org/wiki/XLink
|
||||
-->
|
||||
<nex:nexml
|
||||
version="0.9"
|
||||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||
generator="mesquite"
|
||||
xmlns:xlink="http://www.w3.org/1999/xlink"
|
||||
xmlns:nex="http://www.nexml.org/2009"
|
||||
xmlns="http://www.nexml.org/2009"
|
||||
xsi:schemaLocation="http://www.nexml.org/2009 ../xsd/nexml.xsd">
|
||||
<!--
|
||||
The taxa element is analogous to the taxa block in nexus
|
||||
files. Like all elements that capture things that might
|
||||
need to be referred to elsewhere, it requires an 'id'
|
||||
attribute, whose value must consist of a string of alpha-
|
||||
numeric characters, starting with a letter. In addition,
|
||||
it may (optionally) have the following attributes:
|
||||
* 'label', a free form string, only meant for humans
|
||||
* 'xml:base', indicating the base url of the resource
|
||||
* 'xml:lang', indicating a two-letter language code
|
||||
* 'xml:id', a file-scope unique ID
|
||||
* 'xlink:href', a link to somewhere else
|
||||
* 'class', a vector of nexml id references pointing
|
||||
to classes the element belongs to (this is analogous
|
||||
to 'sets' in nexus, but using the xml idiom to do
|
||||
the same thing).
|
||||
-->
|
||||
<otus
|
||||
id="taxa1"
|
||||
label="My taxa block"
|
||||
xml:base="http://example.org/"
|
||||
xml:id="taxa1"
|
||||
xml:lang="EN"
|
||||
xlink:href="#taxa1">
|
||||
<!--
|
||||
The taxon element is analogous to a single label in
|
||||
a nexus taxa block. It may have the same additional
|
||||
attributes (label, xml:base, xml:lang, xml:id, xlink:href
|
||||
and class) as the taxa element.
|
||||
-->
|
||||
<otu id="t1"/>
|
||||
<otu id="t2"/>
|
||||
<otu id="t3"/>
|
||||
<otu id="t4"/>
|
||||
<otu id="t5"/>
|
||||
</otus>
|
||||
</nex:nexml>
|
||||
283
Tests/NeXML/timetree.xml
Normal file
283
Tests/NeXML/timetree.xml
Normal file
@ -0,0 +1,283 @@
|
||||
<nex:nexml
|
||||
generator="Bio::Phylo::Project v.0.17_RC9_841"
|
||||
version="0.9"
|
||||
xml:base="http://example.org/"
|
||||
xmlns:nex="http://www.nexml.org/2009"
|
||||
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns"
|
||||
xmlns:xml="http://www.w3.org/XML/1998/namespace"
|
||||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||
xsi:schemaLocation="http://www.nexml.org/2009 ../xsd/nexml.xsd"
|
||||
xmlns="http://www.nexml.org/2009">
|
||||
<otus id="otus3">
|
||||
<otu id="taxona"/>
|
||||
<otu id="taxonb"/>
|
||||
</otus>
|
||||
<trees id="trees2" otus="otus3">
|
||||
<tree id="tree6" xsi:type="nex:FloatTree">
|
||||
<node id="node12" root="true"/>
|
||||
<node id="node13" label="Pan" otu="taxona"/>
|
||||
<node id="node14" label="Homo" otu="taxonb"/>
|
||||
<edge id="edge13" length="6.6" source="node12" target="node13"/>
|
||||
<edge id="edge14" length="6.6" source="node12" target="node14"/>
|
||||
</tree>
|
||||
<tree id="tree15" xsi:type="nex:FloatTree">
|
||||
<node id="node21" root="true"/>
|
||||
<node id="node22" label="Pan" otu="taxona"/>
|
||||
<node id="node23" label="Homo" otu="taxonb"/>
|
||||
<edge id="edge22" length="5.8" source="node21" target="node22"/>
|
||||
<edge id="edge23" length="5.8" source="node21" target="node23"/>
|
||||
</tree>
|
||||
<tree id="tree24" xsi:type="nex:FloatTree">
|
||||
<node id="node30" root="true"/>
|
||||
<node id="node31" label="Pan" otu="taxona"/>
|
||||
<node id="node32" label="Homo" otu="taxonb"/>
|
||||
<edge id="edge31" length="6.1" source="node30" target="node31"/>
|
||||
<edge id="edge32" length="6.1" source="node30" target="node32"/>
|
||||
</tree>
|
||||
<tree id="tree33" xsi:type="nex:FloatTree">
|
||||
<node id="node39" root="true"/>
|
||||
<node id="node40" label="Pan" otu="taxona"/>
|
||||
<node id="node41" label="Homo" otu="taxonb"/>
|
||||
<edge id="edge40" length="6.8" source="node39" target="node40"/>
|
||||
<edge id="edge41" length="6.8" source="node39" target="node41"/>
|
||||
</tree>
|
||||
<tree id="tree42" xsi:type="nex:FloatTree">
|
||||
<node id="node48" root="true"/>
|
||||
<node id="node49" label="Pan" otu="taxona"/>
|
||||
<node id="node50" label="Homo sapiens" otu="taxonb"/>
|
||||
<edge id="edge49" length="6.3" source="node48" target="node49"/>
|
||||
<edge id="edge50" length="6.3" source="node48" target="node50"/>
|
||||
</tree>
|
||||
<tree id="tree51" xsi:type="nex:FloatTree">
|
||||
<node id="node57" root="true"/>
|
||||
<node id="node58" label="Pan" otu="taxona"/>
|
||||
<node id="node59" label="Homo sapiens" otu="taxonb"/>
|
||||
<edge id="edge58" length="8.1" source="node57" target="node58"/>
|
||||
<edge id="edge59" length="8.1" source="node57" target="node59"/>
|
||||
</tree>
|
||||
<tree id="tree60" xsi:type="nex:IntTree">
|
||||
<node id="node66" root="true"/>
|
||||
<node id="node67" label="Pan" otu="taxona"/>
|
||||
<node id="node68" label="Homo" otu="taxonb"/>
|
||||
<edge id="edge67" length="6" source="node66" target="node67"/>
|
||||
<edge id="edge68" length="6" source="node66" target="node68"/>
|
||||
</tree>
|
||||
<tree id="tree69" xsi:type="nex:FloatTree">
|
||||
<node id="node75" root="true"/>
|
||||
<node id="node76" label="Pan troglodytes" otu="taxona"/>
|
||||
<node id="node77" label="Homo sapiens" otu="taxonb"/>
|
||||
<edge id="edge76" length="5.1" source="node75" target="node76"/>
|
||||
<edge id="edge77" length="5.1" source="node75" target="node77"/>
|
||||
</tree>
|
||||
<tree id="tree78" xsi:type="nex:FloatTree">
|
||||
<node id="node84" root="true"/>
|
||||
<node id="node85" label="Pan troglodytes" otu="taxona"/>
|
||||
<node id="node86" label="Homo sapiens" otu="taxonb"/>
|
||||
<edge id="edge85" length="5.1" source="node84" target="node85"/>
|
||||
<edge id="edge86" length="5.1" source="node84" target="node86"/>
|
||||
</tree>
|
||||
<tree id="tree87" xsi:type="nex:FloatTree">
|
||||
<node id="node93" root="true"/>
|
||||
<node id="node94" label="Pan troglodytes" otu="taxona"/>
|
||||
<node id="node95" label="Homo sapiens" otu="taxonb"/>
|
||||
<edge id="edge94" length="5.4" source="node93" target="node94"/>
|
||||
<edge id="edge95" length="5.4" source="node93" target="node95"/>
|
||||
</tree>
|
||||
<tree id="tree96" xsi:type="nex:FloatTree">
|
||||
<node id="node102" root="true"/>
|
||||
<node id="node103" label="Pan troglodytes" otu="taxona"/>
|
||||
<node id="node104" label="Homo sapiens" otu="taxonb"/>
|
||||
<edge id="edge103" length="7.5" source="node102" target="node103"/>
|
||||
<edge id="edge104" length="7.5" source="node102" target="node104"/>
|
||||
</tree>
|
||||
<tree id="tree105" xsi:type="nex:FloatTree">
|
||||
<node id="node111" root="true"/>
|
||||
<node id="node112" label="Pan troglodytes" otu="taxona"/>
|
||||
<node id="node113" label="Homo sapiens" otu="taxonb"/>
|
||||
<edge id="edge112" length="7.6" source="node111" target="node112"/>
|
||||
<edge id="edge113" length="7.6" source="node111" target="node113"/>
|
||||
</tree>
|
||||
<tree id="tree114" xsi:type="nex:FloatTree">
|
||||
<node id="node120" root="true"/>
|
||||
<node id="node121" label="Pan" otu="taxona"/>
|
||||
<node id="node122" label="Homo sapiens" otu="taxonb"/>
|
||||
<edge id="edge121" length="7.4" source="node120" target="node121"/>
|
||||
<edge id="edge122" length="7.4" source="node120" target="node122"/>
|
||||
</tree>
|
||||
<tree id="tree123" xsi:type="nex:FloatTree">
|
||||
<node id="node129" root="true"/>
|
||||
<node id="node130" label="Pan troglodytes" otu="taxona"/>
|
||||
<node id="node131" label="Homo sapiens" otu="taxonb"/>
|
||||
<edge id="edge130" length="7.1" source="node129" target="node130"/>
|
||||
<edge id="edge131" length="7.1" source="node129" target="node131"/>
|
||||
</tree>
|
||||
<tree id="tree132" xsi:type="nex:FloatTree">
|
||||
<node id="node138" root="true"/>
|
||||
<node id="node139" label="Pan troglodytes" otu="taxona"/>
|
||||
<node id="node140" label="Homo sapiens" otu="taxonb"/>
|
||||
<edge id="edge139" length="7.1" source="node138" target="node139"/>
|
||||
<edge id="edge140" length="7.1" source="node138" target="node140"/>
|
||||
</tree>
|
||||
<tree id="tree141" xsi:type="nex:FloatTree">
|
||||
<node id="node147" root="true"/>
|
||||
<node id="node148" label="Pan troglodytes" otu="taxona"/>
|
||||
<node id="node149" label="Homo sapiens" otu="taxonb"/>
|
||||
<edge id="edge148" length="8.3" source="node147" target="node148"/>
|
||||
<edge id="edge149" length="8.3" source="node147" target="node149"/>
|
||||
</tree>
|
||||
<tree id="tree150" xsi:type="nex:FloatTree">
|
||||
<node id="node156" root="true"/>
|
||||
<node id="node157" label="Pan troglodytes" otu="taxona"/>
|
||||
<node id="node158" label="Homo sapiens" otu="taxonb"/>
|
||||
<edge id="edge157" length="9.2" source="node156" target="node157"/>
|
||||
<edge id="edge158" length="9.2" source="node156" target="node158"/>
|
||||
</tree>
|
||||
<tree id="tree159" xsi:type="nex:IntTree">
|
||||
<node id="node165" root="true"/>
|
||||
<node id="node166" label="Pan" otu="taxona"/>
|
||||
<node id="node167" label="Homo" otu="taxonb"/>
|
||||
<edge id="edge166" length="11" source="node165" target="node166"/>
|
||||
<edge id="edge167" length="11" source="node165" target="node167"/>
|
||||
</tree>
|
||||
<tree id="tree168" xsi:type="nex:FloatTree">
|
||||
<node id="node174" root="true"/>
|
||||
<node id="node175" label="Pan troglodytes" otu="taxona"/>
|
||||
<node id="node176" label="Homo sapiens" otu="taxonb"/>
|
||||
<edge id="edge175" length="6.2" source="node174" target="node175"/>
|
||||
<edge id="edge176" length="6.2" source="node174" target="node176"/>
|
||||
</tree>
|
||||
<tree id="tree177" xsi:type="nex:FloatTree">
|
||||
<node id="node183" root="true"/>
|
||||
<node id="node184" label="Pan troglodytes" otu="taxona"/>
|
||||
<node id="node185" label="Homo sapiens" otu="taxonb"/>
|
||||
<edge id="edge184" length="5.2" source="node183" target="node184"/>
|
||||
<edge id="edge185" length="5.2" source="node183" target="node185"/>
|
||||
</tree>
|
||||
<tree id="tree186" xsi:type="nex:FloatTree">
|
||||
<node id="node192" root="true"/>
|
||||
<node id="node193" label="Pan troglodytes" otu="taxona"/>
|
||||
<node id="node194" label="Homo sapiens" otu="taxonb"/>
|
||||
<edge id="edge193" length="5.4" source="node192" target="node193"/>
|
||||
<edge id="edge194" length="5.4" source="node192" target="node194"/>
|
||||
</tree>
|
||||
<tree id="tree195" xsi:type="nex:FloatTree">
|
||||
<node id="node201" root="true"/>
|
||||
<node id="node202" label="Pan troglodytes" otu="taxona"/>
|
||||
<node id="node203" label="Homo sapiens" otu="taxonb"/>
|
||||
<edge id="edge202" length="5.6" source="node201" target="node202"/>
|
||||
<edge id="edge203" length="5.6" source="node201" target="node203"/>
|
||||
</tree>
|
||||
<tree id="tree204" xsi:type="nex:FloatTree">
|
||||
<node id="node210" root="true"/>
|
||||
<node id="node211" label="Pan troglodytes" otu="taxona"/>
|
||||
<node id="node212" label="Homo sapiens" otu="taxonb"/>
|
||||
<edge id="edge211" length="7.3" source="node210" target="node211"/>
|
||||
<edge id="edge212" length="7.3" source="node210" target="node212"/>
|
||||
</tree>
|
||||
<tree id="tree213" xsi:type="nex:FloatTree">
|
||||
<node id="node219" root="true"/>
|
||||
<node id="node220" label="Pan troglodytes" otu="taxona"/>
|
||||
<node id="node221" label="Homo sapiens" otu="taxonb"/>
|
||||
<edge id="edge220" length="7.4" source="node219" target="node220"/>
|
||||
<edge id="edge221" length="7.4" source="node219" target="node221"/>
|
||||
</tree>
|
||||
<tree id="tree222" xsi:type="nex:FloatTree">
|
||||
<node id="node228" root="true"/>
|
||||
<node id="node229" label="Pan" otu="taxona"/>
|
||||
<node id="node230" label="Homo sapiens" otu="taxonb"/>
|
||||
<edge id="edge229" length="6.6" source="node228" target="node229"/>
|
||||
<edge id="edge230" length="6.6" source="node228" target="node230"/>
|
||||
</tree>
|
||||
<tree id="tree231" xsi:type="nex:FloatTree">
|
||||
<node id="node237" root="true"/>
|
||||
<node id="node238" label="Pan troglodytes" otu="taxona"/>
|
||||
<node id="node239" label="Homo sapiens" otu="taxonb"/>
|
||||
<edge id="edge238" length="5.41" source="node237" target="node238"/>
|
||||
<edge id="edge239" length="5.41" source="node237" target="node239"/>
|
||||
</tree>
|
||||
<tree id="tree240" xsi:type="nex:FloatTree">
|
||||
<node id="node246" root="true"/>
|
||||
<node id="node247" label="Pan troglodytes" otu="taxona"/>
|
||||
<node id="node248" label="Homo sapiens" otu="taxonb"/>
|
||||
<edge id="edge247" length="6.7" source="node246" target="node247"/>
|
||||
<edge id="edge248" length="6.7" source="node246" target="node248"/>
|
||||
</tree>
|
||||
<tree id="tree249" xsi:type="nex:FloatTree">
|
||||
<node id="node255" root="true"/>
|
||||
<node id="node256" label="Pan" otu="taxona"/>
|
||||
<node id="node257" label="Homo" otu="taxonb"/>
|
||||
<edge id="edge256" length="4.3" source="node255" target="node256"/>
|
||||
<edge id="edge257" length="4.3" source="node255" target="node257"/>
|
||||
</tree>
|
||||
<tree id="tree258" xsi:type="nex:IntTree">
|
||||
<node id="node264" root="true"/>
|
||||
<node id="node265" label="Pan" otu="taxona"/>
|
||||
<node id="node266" label="Homo" otu="taxonb"/>
|
||||
<edge id="edge265" length="13" source="node264" target="node265"/>
|
||||
<edge id="edge266" length="13" source="node264" target="node266"/>
|
||||
</tree>
|
||||
<tree id="tree267" xsi:type="nex:FloatTree">
|
||||
<node id="node273" root="true"/>
|
||||
<node id="node274" label="Pan troglodytes" otu="taxona"/>
|
||||
<node id="node275" label="Homo sapiens" otu="taxonb"/>
|
||||
<edge id="edge274" length="5.5" source="node273" target="node274"/>
|
||||
<edge id="edge275" length="5.5" source="node273" target="node275"/>
|
||||
</tree>
|
||||
<tree id="tree276" xsi:type="nex:FloatTree">
|
||||
<node id="node282" root="true"/>
|
||||
<node id="node283" label="Pan troglodytes" otu="taxona"/>
|
||||
<node id="node284" label="Homo sapiens" otu="taxonb"/>
|
||||
<edge id="edge283" length="3.6" source="node282" target="node283"/>
|
||||
<edge id="edge284" length="3.6" source="node282" target="node284"/>
|
||||
</tree>
|
||||
<tree id="tree285" xsi:type="nex:IntTree">
|
||||
<node id="node291" root="true"/>
|
||||
<node id="node292" label="Pan troglodytes" otu="taxona"/>
|
||||
<node id="node293" label="Homo sapiens" otu="taxonb"/>
|
||||
<edge id="edge292" length="4" source="node291" target="node292"/>
|
||||
<edge id="edge293" length="4" source="node291" target="node293"/>
|
||||
</tree>
|
||||
<tree id="tree294" xsi:type="nex:FloatTree">
|
||||
<node id="node300" root="true"/>
|
||||
<node id="node301" label="Pan" otu="taxona"/>
|
||||
<node id="node302" label="Homo sapiens" otu="taxonb"/>
|
||||
<edge id="edge301" length="5.12" source="node300" target="node301"/>
|
||||
<edge id="edge302" length="5.12" source="node300" target="node302"/>
|
||||
</tree>
|
||||
<tree id="tree303" xsi:type="nex:FloatTree">
|
||||
<node id="node309" root="true"/>
|
||||
<node id="node310" label="Pan" otu="taxona"/>
|
||||
<node id="node311" label="Homo sapiens" otu="taxonb"/>
|
||||
<edge id="edge310" length="5.55" source="node309" target="node310"/>
|
||||
<edge id="edge311" length="5.55" source="node309" target="node311"/>
|
||||
</tree>
|
||||
<tree id="tree312" xsi:type="nex:FloatTree">
|
||||
<node id="node318" root="true"/>
|
||||
<node id="node319" label="Pan troglodytes" otu="taxona"/>
|
||||
<node id="node320" label="Homo sapiens" otu="taxonb"/>
|
||||
<edge id="edge319" length="4.87" source="node318" target="node319"/>
|
||||
<edge id="edge320" length="4.87" source="node318" target="node320"/>
|
||||
</tree>
|
||||
<tree id="tree321" xsi:type="nex:FloatTree">
|
||||
<node id="node327" root="true"/>
|
||||
<node id="node328" label="Pan troglodytes" otu="taxona"/>
|
||||
<node id="node329" label="Homo sapiens" otu="taxonb"/>
|
||||
<edge id="edge328" length="6.4" source="node327" target="node328"/>
|
||||
<edge id="edge329" length="6.4" source="node327" target="node329"/>
|
||||
</tree>
|
||||
<tree id="tree330" xsi:type="nex:FloatTree">
|
||||
<node id="node336" root="true"/>
|
||||
<node id="node337" label="Pan" otu="taxona"/>
|
||||
<node id="node338" label="Homo sapiens" otu="taxonb"/>
|
||||
<edge id="edge337" length="10.4" source="node336" target="node337"/>
|
||||
<edge id="edge338" length="10.4" source="node336" target="node338"/>
|
||||
</tree>
|
||||
<tree id="tree339" xsi:type="nex:FloatTree">
|
||||
<node id="node345" root="true"/>
|
||||
<node id="node346" label="Pan" otu="taxona"/>
|
||||
<node id="node347" label="Homo sapiens" otu="taxonb"/>
|
||||
<edge id="edge346" length="13.7" source="node345" target="node346"/>
|
||||
<edge id="edge347" length="13.7" source="node345" target="node347"/>
|
||||
</tree>
|
||||
</trees>
|
||||
</nex:nexml>
|
||||
49
Tests/NeXML/tolweb.xml
Normal file
49
Tests/NeXML/tolweb.xml
Normal file
@ -0,0 +1,49 @@
|
||||
<nex:nexml
|
||||
generator="Bio::Phylo::Project v.0.21_1265"
|
||||
version="0.9"
|
||||
xmlns="http://www.nexml.org/2009"
|
||||
xml:base="http://example.org/"
|
||||
xmlns:dc="http://purl.org/dc/elements/1.1/contributor"
|
||||
xmlns:dcterms="http://purl.org/dc/terms/"
|
||||
xmlns:nex="http://www.nexml.org/2009"
|
||||
xmlns:owl="http://www.w3.org/2002/07/owl#"
|
||||
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
|
||||
xmlns:tba="http://tolweb.org/tree/home.pages/downloadtree.html#"
|
||||
xmlns:tbe="http://tolweb.org/tree/home.pages/downloadtree.html#"
|
||||
xmlns:xml="http://www.w3.org/XML/1998/namespace"
|
||||
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
|
||||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||
xsi:schemaLocation="http://www.nexml.org/2009 ../xsd/nexml.xsd">
|
||||
<otus id="otus26">
|
||||
<otu id="otu27" label="Eurysphindus"/>
|
||||
</otus>
|
||||
<trees about="#trees22" id="trees22" otus="otus26">
|
||||
<meta content="117855" datatype="xsd:integer" id="meta24" property="dcterms:identifier" xsi:type="nex:LiteralMeta"/>
|
||||
<meta href="http://tolweb.org/117855" id="meta25" rel="owl:sameAs" xsi:type="nex:ResourceMeta"/>
|
||||
<tree id="tree1" xsi:type="nex:IntTree">
|
||||
<node about="#node2" id="node2" root="true">
|
||||
<meta content="117851" datatype="xsd:integer" id="meta21" property="tba:ID" xsi:type="nex:LiteralMeta"/>
|
||||
</node>
|
||||
<node about="#node3" id="node3" label="Eurysphindus" otu="otu27">
|
||||
<meta content="" datatype="xsd:string" id="meta4" property="dc:description" xsi:type="nex:LiteralMeta"/>
|
||||
<meta content="Leconte" datatype="xsd:string" id="meta5" property="tbe:AUTHORITY" xsi:type="nex:LiteralMeta"/>
|
||||
<meta content="1878" datatype="xsd:integer" id="meta6" property="tbe:AUTHDATE" xsi:type="nex:LiteralMeta"/>
|
||||
<meta content="117851" datatype="xsd:integer" id="meta7" property="tba:ANCESTORWITHPAGE" xsi:type="nex:LiteralMeta"/>
|
||||
<meta content="0" datatype="xsd:integer" id="meta8" property="tba:CHILDCOUNT" xsi:type="nex:LiteralMeta"/>
|
||||
<meta content="null" datatype="xsd:string" id="meta9" property="tba:COMBINATION_DATE" xsi:type="nex:LiteralMeta"/>
|
||||
<meta content="0" datatype="xsd:integer" id="meta10" property="tba:CONFIDENCE" xsi:type="nex:LiteralMeta"/>
|
||||
<meta content="0" datatype="xsd:integer" id="meta11" property="tba:EXTINCT" xsi:type="nex:LiteralMeta"/>
|
||||
<meta content="1" datatype="xsd:integer" id="meta12" property="tba:HASPAGE" xsi:type="nex:LiteralMeta"/>
|
||||
<meta content="117855" datatype="xsd:integer" id="meta13" property="tba:ID" xsi:type="nex:LiteralMeta"/>
|
||||
<meta content="0" datatype="xsd:integer" id="meta14" property="tba:INCOMPLETESUBGROUPS" xsi:type="nex:LiteralMeta"/>
|
||||
<meta content="0" datatype="xsd:integer" id="meta15" property="tba:IS_NEW_COMBINATION" xsi:type="nex:LiteralMeta"/>
|
||||
<meta content="1" datatype="xsd:integer" id="meta16" property="tba:ITALICIZENAME" xsi:type="nex:LiteralMeta"/>
|
||||
<meta content="0" datatype="xsd:integer" id="meta17" property="tba:LEAF" xsi:type="nex:LiteralMeta"/>
|
||||
<meta content="0" datatype="xsd:integer" id="meta18" property="tba:PHYLESIS" xsi:type="nex:LiteralMeta"/>
|
||||
<meta content="0" datatype="xsd:integer" id="meta19" property="tba:SHOWAUTHORITY" xsi:type="nex:LiteralMeta"/>
|
||||
<meta content="1" datatype="xsd:integer" id="meta20" property="tba:SHOWAUTHORITYCONTAINING" xsi:type="nex:LiteralMeta"/>
|
||||
</node>
|
||||
<edge id="edge3" source="node2" target="node3"/>
|
||||
</tree>
|
||||
</trees>
|
||||
</nex:nexml>
|
||||
2062
Tests/NeXML/treebase-record.xml
Normal file
2062
Tests/NeXML/treebase-record.xml
Normal file
File diff suppressed because it is too large
Load Diff
39
Tests/NeXML/trees-uris.xml
Normal file
39
Tests/NeXML/trees-uris.xml
Normal file
@ -0,0 +1,39 @@
|
||||
<?xml version="1.0" encoding="ISO-8859-1"?>
|
||||
<nex:nexml
|
||||
version="0.9"
|
||||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||
xmlns:xml="http://www.w3.org/XML/1998/namespace"
|
||||
xsi:schemaLocation="http://www.nexml.org/2009 ../xsd/nexml.xsd"
|
||||
xmlns:nex="http://www.nexml.org/2009"
|
||||
xmlns:cdao="http://www.evolutionaryontology.org/cdao/1.0/cdao.owl#"
|
||||
xmlns:xsd="http://www.w3.org/2001/XMLSchema"
|
||||
xmlns="http://www.nexml.org/2009">
|
||||
<otus id="tax1" xml:base="http://example.org/taxon/TB2:">
|
||||
<otu id="t1"/>
|
||||
<otu id="t2"/>
|
||||
<otu id="t3"/>
|
||||
<otu id="t4"/>
|
||||
<otu id="t5"/>
|
||||
</otus>
|
||||
<trees otus="tax1" id="Trees" xml:base="http://example.org/tree/TB2:">
|
||||
<tree id="tree1" xsi:type="nex:FloatTree">
|
||||
<node id="n1" root="true"/>
|
||||
<node id="n2" otu="t1"/>
|
||||
<node id="n3"/>
|
||||
<node id="n4"/>
|
||||
<node id="n5" otu="t3"/>
|
||||
<node id="n6" otu="t2"/>
|
||||
<node id="n7"/>
|
||||
<node id="n8" otu="t5"/>
|
||||
<node id="n9" otu="t4"/>
|
||||
<edge source="n1" target="n3" id="e1" length="0.34534"/>
|
||||
<edge source="n1" target="n2" id="e2" length="0.4353"/>
|
||||
<edge source="n3" target="n4" id="e3" length="0.324"/>
|
||||
<edge source="n3" target="n7" id="e4" length="0.3247"/>
|
||||
<edge source="n4" target="n5" id="e5" length="0.234"/>
|
||||
<edge source="n4" target="n6" id="e6" length="0.3243"/>
|
||||
<edge source="n7" target="n8" id="e7" length="0.32443"/>
|
||||
<edge source="n7" target="n9" id="e8" length="0.2342"/>
|
||||
</tree>
|
||||
</trees>
|
||||
</nex:nexml>
|
||||
127
Tests/NeXML/trees.xml
Normal file
127
Tests/NeXML/trees.xml
Normal file
@ -0,0 +1,127 @@
|
||||
<?xml version="1.0" encoding="ISO-8859-1"?>
|
||||
<!--
|
||||
For an explanation of the structure of the root element
|
||||
and the taxa element refer to the file taxa.xml.
|
||||
-->
|
||||
<nex:nexml
|
||||
version="0.9"
|
||||
xml:base="http://example.org/"
|
||||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||
xmlns:xml="http://www.w3.org/XML/1998/namespace"
|
||||
xsi:schemaLocation="http://www.nexml.org/2009 ../xsd/nexml.xsd"
|
||||
xmlns:nex="http://www.nexml.org/2009"
|
||||
xmlns:cdao="http://www.evolutionaryontology.org/cdao/1.0/cdao.owl#"
|
||||
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
|
||||
xmlns="http://www.nexml.org/2009">
|
||||
<otus id="tax1" label="RootTaxaBlock">
|
||||
<otu id="t1"/>
|
||||
<otu id="t2"/>
|
||||
<otu id="t3"/>
|
||||
<otu id="t4"/>
|
||||
<otu id="t5"/>
|
||||
</otus>
|
||||
<!--
|
||||
The trees block is structured as follows:
|
||||
* the root element takes the same attributes as
|
||||
characters elements do: an id, a reference
|
||||
to a taxa element, and various optional
|
||||
attributes.
|
||||
* the trees element contains one or more tree/network
|
||||
elements, which are the same structure as
|
||||
GraphML documents (http://graphml.graphdrawing.org/),
|
||||
with the following extentions:
|
||||
- there are two subclasses (xsi:type="nex:Tree" and
|
||||
xsi:type="nex:Network"), which only differ in the
|
||||
constrained in-degree of node elements (one for
|
||||
trees, one or more for networks)
|
||||
- node elements can have an additional taxon attribute
|
||||
to refer to a taxon element defined earlier
|
||||
- edge elements can have a 'length' attribute
|
||||
to specify edge length/weight, which is a
|
||||
IEEE 754-1985 compliant floating point number on
|
||||
trees of type FloatTree.
|
||||
-->
|
||||
<trees otus="tax1" id="Trees" label="TreesBlockFromXML">
|
||||
<!--
|
||||
A tree with float edges.
|
||||
-->
|
||||
<tree id="tree1" xsi:type="nex:FloatTree" label="tree1">
|
||||
<node id="n1" label="n1" root="true"/>
|
||||
<node id="n2" label="n2" otu="t1"/>
|
||||
<node id="n3" label="n3"/>
|
||||
<node id="n4" label="n4" about="#n4">
|
||||
<meta
|
||||
id="dict1"
|
||||
property="cdao:has_tag"
|
||||
content="true"
|
||||
xsi:type="nex:LiteralMeta"
|
||||
datatype="xsd:boolean"/>
|
||||
</node>
|
||||
<node id="n5" label="n5" otu="t3"/>
|
||||
<node id="n6" label="n6" otu="t2"/>
|
||||
<node id="n7" label="n7"/>
|
||||
<node id="n8" label="n8" otu="t5"/>
|
||||
<node id="n9" label="n9" otu="t4"/>
|
||||
<edge source="n1" target="n3" id="e1" length="0.34534"/>
|
||||
<edge source="n1" target="n2" id="e2" length="0.4353"/>
|
||||
<edge source="n3" target="n4" id="e3" length="0.324"/>
|
||||
<edge source="n3" target="n7" id="e4" length="0.3247"/>
|
||||
<edge source="n4" target="n5" id="e5" length="0.234"/>
|
||||
<edge source="n4" target="n6" id="e6" length="0.3243"/>
|
||||
<edge source="n7" target="n8" id="e7" length="0.32443"/>
|
||||
<edge source="n7" target="n9" id="e8" length="0.2342"/>
|
||||
</tree>
|
||||
<!--
|
||||
A tree with int edges.
|
||||
-->
|
||||
<tree id="tree2" xsi:type="nex:IntTree" label="tree2">
|
||||
<node id="tree2n1" label="n1"/>
|
||||
<node id="tree2n2" label="n2" otu="t1"/>
|
||||
<node id="tree2n3" label="n3"/>
|
||||
<node id="tree2n4" about="#tree2n4" label="n4">
|
||||
<meta
|
||||
id="tree2dict1"
|
||||
property="cdao:has_tag"
|
||||
content="true"
|
||||
xsi:type="nex:LiteralMeta"
|
||||
datatype="xsd:boolean"/>
|
||||
</node>
|
||||
<node id="tree2n5" label="n5" otu="t3"/>
|
||||
<node id="tree2n6" label="n6" otu="t2"/>
|
||||
<node id="tree2n7" label="n7"/>
|
||||
<node id="tree2n8" label="n8" otu="t5"/>
|
||||
<node id="tree2n9" label="n9" otu="t4"/>
|
||||
<edge source="tree2n1" target="tree2n3" id="tree2e1" length="1"/>
|
||||
<edge source="tree2n1" target="tree2n2" id="tree2e2" length="2"/>
|
||||
<edge source="tree2n3" target="tree2n4" id="tree2e3" length="3"/>
|
||||
<edge source="tree2n3" target="tree2n7" id="tree2e4" length="1"/>
|
||||
<edge source="tree2n4" target="tree2n5" id="tree2e5" length="2"/>
|
||||
<edge source="tree2n4" target="tree2n6" id="tree2e6" length="1"/>
|
||||
<edge source="tree2n7" target="tree2n8" id="tree2e7" length="1"/>
|
||||
<edge source="tree2n7" target="tree2n9" id="tree2e8" length="1"/>
|
||||
</tree>
|
||||
<!--
|
||||
A network with int edges.
|
||||
-->
|
||||
<network id="tree3" xsi:type="nex:IntNetwork" label="tree2">
|
||||
<node id="tree3n1" label="tree3n1"/>
|
||||
<node id="tree3n2" label="tree3n2" otu="t1"/>
|
||||
<node id="tree3n3" label="tree3n3"/>
|
||||
<node id="tree3n4" label="tree3n4"/>
|
||||
<node id="tree3n5" label="tree3n5" otu="t3"/>
|
||||
<node id="tree3n6" label="tree3n6" otu="t2"/>
|
||||
<node id="tree3n7" label="tree3n7"/>
|
||||
<node id="tree3n8" label="tree3n8" otu="t5"/>
|
||||
<node id="tree3n9" label="tree3n9" otu="t4"/>
|
||||
<edge source="tree3n1" target="tree3n3" id="tree3e1" length="1"/>
|
||||
<edge source="tree3n1" target="tree3n2" id="tree3e2" length="2"/>
|
||||
<edge source="tree3n3" target="tree3n4" id="tree3e3" length="3"/>
|
||||
<edge source="tree3n3" target="tree3n7" id="tree3e4" length="1"/>
|
||||
<edge source="tree3n4" target="tree3n5" id="tree3e5" length="2"/>
|
||||
<edge source="tree3n4" target="tree3n6" id="tree3e6" length="1"/>
|
||||
<edge source="tree3n7" target="tree3n6" id="tree3e7" length="1"/> <!-- extra edge -->
|
||||
<edge source="tree3n7" target="tree3n8" id="tree3e9" length="1"/>
|
||||
<edge source="tree3n7" target="tree3n9" id="tree3e8" length="1"/>
|
||||
</network>
|
||||
</trees>
|
||||
</nex:nexml>
|
||||
73
Tests/test_Phylo_NeXML.py
Normal file
73
Tests/test_Phylo_NeXML.py
Normal file
@ -0,0 +1,73 @@
|
||||
# Copyright (C) 2013 by Ben Morris (ben@bendmorris.com)
|
||||
# based on code by Eric Talevich (eric.talevich@gmail.com)
|
||||
# This code is part of the Biopython distribution and governed by its
|
||||
# license. Please see the LICENSE file that should have been included
|
||||
# as part of this package.
|
||||
|
||||
"""Unit tests for the NeXML and NeXMLIO modules.
|
||||
"""
|
||||
|
||||
import os
|
||||
import tempfile
|
||||
import unittest
|
||||
|
||||
import Bio.Phylo as bp
|
||||
from Bio.Phylo import NeXML, NeXMLIO
|
||||
|
||||
# Example NeXML files
|
||||
example_files = ['NeXML/%s' % f
|
||||
for f in (
|
||||
'characters.xml',
|
||||
'edgelabels.xml',
|
||||
'meta_taxa.xml',
|
||||
'meta_types.xml',
|
||||
'nexml.xml',
|
||||
'phenoscape.xml',
|
||||
'sets.xml',
|
||||
'taxa.xml',
|
||||
'timetree.xml',
|
||||
'tolweb.xml',
|
||||
'treebase-record.xml',
|
||||
'trees-uris.xml',
|
||||
'trees.xml',
|
||||
)]
|
||||
|
||||
# Temporary file name for Writer tests below
|
||||
DUMMY = tempfile.mktemp()
|
||||
|
||||
|
||||
# ---------------------------------------------------------
|
||||
# Parser tests
|
||||
|
||||
def _test_parse_factory(source, count=0):
|
||||
"""Generate a test method for parse()ing the given source.
|
||||
|
||||
The generated function extracts each phylogenetic tree using the parse()
|
||||
function and counts the total number of trees extracted.
|
||||
"""
|
||||
fname = os.path.basename(source)
|
||||
|
||||
def test_parse(self):
|
||||
trees = bp._io.parse(source, 'nexml')
|
||||
#self.assertEqual(len(list(trees)), count)
|
||||
|
||||
test_parse.__doc__ = "Parse the phylogenies in %s." % fname
|
||||
return test_parse
|
||||
|
||||
|
||||
class ParseTests(unittest.TestCase):
|
||||
"""Tests for proper parsing of example phyloXML files."""
|
||||
|
||||
for n, ex in enumerate(example_files):
|
||||
parse_test = _test_parse_factory(ex)
|
||||
parse_test.__name__ = 'test_parse_%s' % n
|
||||
setattr(ParseTests, parse_test.__name__, parse_test)
|
||||
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
runner = unittest.TextTestRunner(verbosity=2)
|
||||
unittest.main(testRunner=runner)
|
||||
# Clean up the temporary file
|
||||
if os.path.exists(DUMMY):
|
||||
os.remove(DUMMY)
|
||||
Reference in New Issue
Block a user