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Full Discussion: Extract data from XML file
Top Forums Shell Programming and Scripting Extract data from XML file Post 302773507 by mohan sharma on Thursday 28th of February 2013 05:44:26 AM
Old 02-28-2013
Extract data from XML file

Hi ,
I have input file as XML. following are input data
#complex.xml
Code:
<?xml version="1.0" encoding="UTF-8"?>
<TEST_doc xmlns="http://www.w3.org/2001/XMLSchema-instance">
  <ENTRY uid="123456">
    <protein>
      <name>PROT001</name>
      <organism>Human</organism>
      <class>cytoplasmic</class>
    </protein>
    <xrefs>
      <xref>
          <database>Ensembl</database>
          <accn>ENSG00000105829</accn>
      </xref>
      <xref>
          <database>UNIPROT</database>
          <accn>Q12345</accn>
      </xref>
    </xrefs>
  </ENTRY>
  <ENTRY uid="45678">
    <protein>
      <name>PROT002</name>
      <organism>Human</organism>
      <class>nuclear</class>
    </protein>
    <xrefs>
      <xref>
          <database>Ensembl</database>
          <accn>ENSG00000105333</accn>
      </xref>
      <xref>
          <database>UNIPROT</database>
          <accn>Q14789</accn>
      </xref>
    </xrefs>
  </ENTRY>
</TEST_doc>

i want to extract data from this file and i tried below query.
cat complex.xml | xml sel -t -m //xref -v "concat(../../protein/name,' ',../../protein/class,' ',./database,' ',./accn)" -n

but it is not giving any output...but this query is working when instead of xmlns i am writing xmlns:xsi="...."
but my input file is having only xmlns="..."

please help me ...

Last edited by fpmurphy; 02-28-2013 at 09:53 AM..
 

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XML::Easy::Transform(3pm)				User Contributed Perl Documentation				 XML::Easy::Transform(3pm)

NAME
XML::Easy::Tranform - XML processing with a clean interface DESCRIPTION
The "XML::Easy::Transform::" namespace exists to contain modules that perform transformations on XML documents, or parts thereof, in the form of XML::Easy::Element and XML::Easy::Content nodes. XML::Easy is a collection of modules relating to the processing of XML data. It includes functions to parse and serialise the standard textual form of XML. When XML data is not in text form, XML::Easy processes it in an abstract syntax-neutral form, as a collection of linked Perl objects. This in-program data format shields XML users from the infelicities of XML syntax. Modules under the "XML::Easy::Transform::" namespace operate on XML data in this abstract structured form, not on textual XML. A transformation on XML data should normally be presented in the form of a function, which takes an XML::Easy::Element node as its main parameter, and returns an XML::Easy::Element node (or "die"s on error). The input node and output node each represent the root element of the XML document (or fragment thereof) being transformed. These nodes, of course, contain subordinate nodes, according to the structure of the XML data. A reference to the top node is all that is required to effectively pass the whole document. OTHER DISTRIBUTIONS
CPAN distributions under this namespace are: XML::Easy::Transform::RationalizeNamespacePrefixes Manages XML Namespaces by hoisting all namespace declarations to the root of a document. SEE ALSO
XML::Easy AUTHOR
Andrew Main (Zefram) <zefram@fysh.org> COPYRIGHT
Copyright (C) 2009, 2010, 2011 Andrew Main (Zefram) <zefram@fysh.org> LICENSE
This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself. perl v5.14.2 2011-11-16 XML::Easy::Transform(3pm)
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