Masterarbeit, Heidi Lischer

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====== PGD file example ======
Unaligned data with mixed number of reads:
<code>
<?xml version="1.0" encoding="iso-8859-1" ?> 
<?xml-stylesheet type="text/xsl" href="stylesheet_PGD.xsl"?>

<PGD>

  <header title="faked example data">
    <organism> homo sapiens sapiens </organism>
    <numPop> 3 </numPop>
    <ploidy> 1 </ploidy>
    <aligned> no </aligned>
    <missing> ? </missing>
    <gap> - </gap>
  </header>

  <dataDescription>
    <numLoci> 2 </numLoci>
    <dataType> DNA </dataType> 
    <locus id="loci one">
      <locusChromosome> 3 </locusChromosome>
      <locusLocation> Hs8_23892 </locusLocation> 
      <locusGenic> coding </locusGenic>
      <locusLinks> www.loci.ch/faked_adress/ </locusLinks>
      <locusComments> faked </locusComments>
    </locus>
    <locus id="loci two">
      <locusChromosom> 3 </locusChromosom>
      <locusLocation> Hs8_23992 </locusLocation> 
      <locusGenic> noncoding </locusGenic>
    </locus>
  </dataDescription>

  <population name="pop 1">
    <popSize> 3 </popSize>
    <ind name="1">
      <indGeogCoord> 35, 4 </indGeogCoord>
      <indLingGroup> African </indLingGroup>
      <indLoci> loci one </indLoci>
      <indFreq> 10 </indFreq>
      <read>
        <start> 230 </start> 
        <length> 100 </length>
        <data> ATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAT </data>
      </read>
      <read>
        <start> 240 </start> 
        <length> 90 </length>
        <data> AAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAT </data>  
      </read>
    </ind>

    <ind name="2">
      <indGeogCoord> 36, 4 </indGeogCoord>
      <indLingGroup> Africanic </indLingGroup>
      <indLoci> loci one </indLoci>
      <indFreq> 11 </indFreq>
      <read>
        <start> 273 </start>
        <length> 57 </length>
        <data> TCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAT </data>
      </read>
    </ind>

    <ind name="3">
      <indGeogCoord> 35, 5 </indGeogCoord>
      <indLingGroup> African </indLingGroup>
      <indLoci> loci one </indLoci>
      <indNumReads> 3 </indNumReads>
      <read>
        <start> 256 </start>
        <length> 74 </length>
        <data> TTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAT </data>
      </read>
      <read>
        <start> 260 </start>
        <length> 70 </length>
        <data> AACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAT </data>
      </read>
      <read>
        <start> 250 </start>
        <length> 80 </length>
        <data> AAACCCTTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAT </data>
      </read>
    </ind>
  </population>

 

  <population name="pop 2">
    <popSize> 2 </popSize>
    <popGeogCoord> 8, 48 </popGeogCoord>
    <popLingGroup> European </popLingGroup>
    <popLoci> loci two </popLoci>
    <ind name="4">
      <read>
        <start> 265 </start> 
        <length> 65 </length>
        <data> TTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAT </data>
      </read>
    </ind>
    <ind name="5">
      <read>
        <start> 250 </start> 
        <length> 80 </length>
        <data> TTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAT </data>        
      </read>
    </ind>
  </population>


  <population name="pop 3">
    <popSize> 3 </popSize>
    <popLoci> loci 3 </popLoci>
    <ind name="1">
      <indGeogCoord> 35, 4 </indGeogCoord>
      <indLingGroup> African </indLingGroup>
      <read>
        <start> 230 </start>
        <length> 100 </length>
        <data> ATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAT </data>
      </read>
      <read>
        <start> 240 </start>
        <length> 90 </length>
        <data> AAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAT </data>  
      </read>
    </ind>

    <ind name="2">
      <indGeogCoord> 36, 4 </indGeogCoord>
      <indLingGroup> Africanic </indLingGroup>
      <indFreq> 10 </indFreq>
      <read>
        <start> 273 </start>
        <length> 57 </length>
        <data> TCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAT </data>
      </read>
    </ind>

    <ind name="3">
      <indGeogCoord> 35, 5 </indGeogCoord>
      <indLingGroup> African </indLingGroup>
      <indNumReads> 3 </indNumReads>
      <read>
        <start> 256 </start>
        <length> 74 </length>
        <data> TTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAT </data>
      </read>
      <read>
        <start> 250 </start>
        <length> 80 </length>
        <data> AAACCCTTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAT </data>
      </read>
      <read>
        <start> 260 </start>
        <length> 65 </length>
        <data> AACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCAT </data>
      </read>
    </ind>
  </population>

  <structure name="faked">
    <numGroups> 2 </numGroups> 
    <group name="one"> pop 1 </group>
    <group name="two"> pop 2, pop 3 </group>
  </structure>

</PGD>
</code>