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#1
02-28-2013
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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 08:53 AM.. |
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#2
02-28-2013
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Please use code tags. Please post the output you are expecting from your sample input.
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| query result |
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