Hi monks-of-perliness, I'm having a problem getting the data out of an xml file with XML::simple.

The xml file contains information in the form:

<project by="company" name="personname">
  <pattern name="company-000001" owner="company" description="Microarr
+ay" species_database="d.base">
    <reporter name="A_24_P344666" systematic_name="NM_020341">
      <feature number="1780">
        <position x="0.733234841870825" y="10.033" units="mm" />
      </feature>
      <gene systematic_name="NM_020341" primary_name="PAK7" descriptio
+n="Homo sapiens p21(CDKN1A)-activated kinase 7 (PAK7), transcript var
+iant 1, mRNA [NM_020341]">
        <accession database="ref" id="NM_020341" />
        <accession database="ref" id="NM_177990" />
        <accession database="ens" id="ENST00000378429" />
        <accession database="ens" id="ENST00000378423" />
        <other name="accessions" value="ref|NM_020341|ref|NM_177990|en
+s|ENST00000378429|ens|ENST00000378423" />
        <other name="chr_coord" value="chr20:9466136-9466077" />
      </gene>
    </reporter>

    <reporter ...
    </reporter>

    <reporter ...
    </reporter>

  </pattern>
</project>

[download]


I want to pick out the different names (instances of name, systematic_name & primary_name) put then into an array and then store this array as a value in a hash with the key being the reporter attribute: name.

If I read this into perl with XML::simple and don't specify KeyAttr, then when I try:  my @probekeys = keys %{$data->{pattern}->{reporter}};

then it tried to use name as the hash keys and reads these into an array (which is what I want) but it falls over because name turns out not to be unique.

If I read this into perl with XML::simple and specify a different attribute as the key attribute using KeyAttr, then when I try:  my @probekeys = keys %{$data->{pattern}->{reporter}};

Then XML::simple insists on forcing things into arrays (even if I use ForceArray => 0) and I keep getting told that pseudo-hashes have been depreciated.... Does anyone have any smart ideas about how I can get hold of this information without just reading the 500k line file in one line at a time?

In reply to XML::Simple and pseudo hashes... by nickschurch

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