XML::Twig

[matth]

Hi Monks,

The code shown in Re: Removing duplicate subtrees from XML works very well with the data shown in this posting. But with my data (as below)

  

<species name = "hs">
 <sequence id = "1" title = "chromosome 1">
  <genome_feature type = "CDS">
   <gene id = "01">
    <gene_seq number = "1"></gene_seq>
   </gene>
  </genome_feature>
 </sequence>
</species>

<species name = "hs">
 <sequence id = "1" title = "chromosome 1">
  <genome_feature type = "CDS">
   <gene id = "17">
    <gene_seq number = "2"></gene_seq>
   </gene>
  </genome_feature>
 </sequence>
</species>

I get the following error messages:

bash-2.05$ perl perl_monks_F.pl
sorted doc generation NOK:
expected:
<species name = "hs">
 <sequence id = "1" title = "chromosome 1">
  <genome_feature type = "CDS">
   <gene id = "17">
    <gene_seq number = "2"></gene_seq>
   </gene>
  </genome_feature>
 </sequence>
</species>
found:
<species name="hs">
  <sequence id="1" title="chromosome 1">
    <genome_feature type="CDS">
      <gene id="01">
        <gene_seq number="1"></gene_seq>
      </gene>
    </genome_feature>
  </sequence>
</species>

Use of uninitialized value in substitution (s///) at perl_monks_F.pl l
+ine 143, <DATA> chunk 2.
Use of uninitialized value in substitution (s///) at perl_monks_F.pl l
+ine 144, <DATA> chunk 2.
Use of uninitialized value in substitution (s///) at perl_monks_F.pl l
+ine 145, <DATA> chunk 2.
Use of uninitialized value in string eq at perl_monks_F.pl line 50, <D
+ATA> chunk 2.
Use of uninitialized value in concatenation (.) or string at perl_monk
+s_F.pl line 56, <DATA> chunk 2.
merged doc generation NOK:
expected:

found:
<species name="hs">
  <sequence id="1" title="chromosome 1">
    <genome_feature type="CDS">
      <gene id="01">
        <gene_seq number="1"></gene_seq>
      </gene>
    </genome_feature>
  </sequence>
</species>

bash-2.05$

Alterations that I made to the provided script were the addition of a few ErrorContext => 1 statements. And I have tested these slight alterations with the data used in the top posting link.

[matth]

I was so focused on the problem that I forgot to ask if anyone could point out the structural difference between the XML data in the above posting and the XML data for mirod's code in Re: Removing duplicate subtrees from XML.

[matth]

I am now doing some debugging work which is finding some obvious answers. I will come back with a report on how to alter the script in question. Hold on everyone.