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How To Filter A Blast Xml Output ?

Hello list, I have very large xml blast outputs (in order to use with blast2go) and I need to reduce these consequently according to a selected criterium (for instance the E-value). Did anybody write a script for it ? If not, I would share mine when it will be done !!

Thanks,

Emmanuel

EDIT : Thank you for the answers. I'm not used in xml file handling, and I accept your proposal Egon ! So here is a subset of my blast xml output: EDIT 2: I removed the example: too big, and combined with the new "markup formatting" it makes the reading of the question very annoying.

It's big but I had to show you several situations (a multi-hsp hit for example). So I want to be able to filter this file using the hsp statistics.

Here is a detailed example of the output shrinkage I would like to conduct:

How would you do if you wanted to delete from the xml the path (including the markups) within
- <Iteration_stat> and </Iteration_stat>
- <Hsp> and </Hsp> if the HSP evalue (<Hsp_evalue>here</Hsp>) is > 1e-20
- <Hit> and </Hit> if all the HSP evalue is > 1e-20
- <Iteration> and </Iteration> if
-- all the HSP evalue is > 1e-20
-- OR there is the <Iteration_message>No hits found</Iteration_message> message
?

Thanks again for help and advice.

Emmanuel

xml blast filter parsing
• 9,963 views • link
written by Manu Prestat Manu Prestat

Please add a full snippet of the XML, including the root element and an element you like to match. That way, people can suggest the proper XPath query.

• 0 views • link
written by Egon Willighagen Egon Willighagen

When you say filter, do you mean make a smaller XML file, or just extract the key data?

• 0 views • link
written by Peter Peter

I mean a smaller XML file (the goal is to use blast2go).

• 0 views • link
written by Manu Prestat Manu Prestat

3 answers

XSLT is really nice, but it might look intimidating at first sight. To overcome this I would suggest to use a command line tool like xmlstarlet (http://xmlstar.sourceforge.net/) to get your results.

When I use your example on the following command line:

cat blastoutput.xml | xmlstarlet sel -t -m //Hsp -v "concat(../../Hit_id,' , ',./Hsp_score, ' , ', ./Hsp_bit-score)" -n

The result is:

gi|17228516|ref|NP_485064.1| , 433 , 171.399648652258
gi|17228516|ref|NP_485064.1| , 233 , 94.3597334687873
gi|159899325|ref|YP_001545572.1| , 433 , 171.399648652258

For other example see the documentation: http://xmlstar.sourceforge.net/doc/UG/xmlstarlet-ug.html

The beauty of xmlstarlet is that your can use it to generate your XSLT files. If you include -C it will not generate the output, but the XSLT file to be used when you would like to apply XSLT.

pbpaste | xmlstarlet sel -C -t -m //Hsp -v "concat(../../Hit_id,' , ',./Hsp_score, ' , ', ./Hsp_bit-score)" -n

<xsl:stylesheet xmlns:xsl="&lt;a href=" http:="" www.w3.org="" 1999="" XSL="" Transform"="" rel="nofollow">http://www.w3.org/1999/XSL/Transform" version="1.0">
  <xsl:output omit-xml-declaration="yes" indent="no"/>
  <xsl:template match="/">
    <xsl:for-each select="//Hsp">
      <xsl:value-of select="concat(../../Hit_id,' , ',./Hsp_score, ' , ', ./Hsp_bit-score)"/>
      <xsl:value-of select="'
'"/>
    </xsl:for-each>
  </xsl:template>
</xsl:stylesheet>
• 1 views • link
updated by Ram Ram • written by Andra Waagmeester Andra Waagmeester

This seems to be a very powerful tool: thank you! I have not written the good query yet, but I have to learn more about that. How would you do if you wanted to delete from the xml the path (including the markups) within

  • [?] and [?]
  • [?] and [?] if the HSP evalue ([?]here[?] 1e-20
  • [?] and [?] if all the HSP evalue is > 1e-20
  • [?] and [?] if
  • all the HSP evalue is > 1e-20
  • OR there is the [?]No hits found[?] message. ?

Emmanuel

• 0 views • link
written by Manu Prestat Manu Prestat

You can use a simple XSLT stylesheet to filter the hsps.

For example, see this other question on biostar Standalone Blast Options that was used to get the very first Hit.

• 1 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

An alternative to XSLT, is to use a XPath query directly, e.g. using the xpath executable from the libxml-xpath-perl package in Debian GNU/Linux. When you added some example XML output, then I could add the appropriate XPath query.

• 0 views • link
written by Egon Willighagen Egon Willighagen

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