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Split a blastp xml output

Hello!

I have an xml output of the blast, which would be used to analyze the Blast2go, however, as early analysis, always comes up the following error message:

Exception in thread "main" java.lang.OutOfMemoryError: Requested array size exceeds VM limit

I was suggested to divide the xml file into smaller files, like I could do this?

xml blast
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updated by Ram Ram • written by Stela Ribeiro • Stela Ribeiro

Hi Pierre,

I used Xmx60000m, I believe that I can not increase more =(

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updated by Ram Ram • written by Stela Ribeiro • Stela Ribeiro

Yess! o //

Thank you Pierre, I will test the tool.

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updated by Ram Ram • written by Stela Ribeiro • Stela Ribeiro

Hi Pierre,

The tool works for separation, However, the files Appear to all be the same, everyone starts describing the hits for the same gene, this is possible? it is possible to fix?

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updated by Ram Ram • written by Stela Ribeiro • Stela Ribeiro

look at your question; You never talked about 'gene'. The tool only split the XML.

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written by Pierre Lindenbaum Pierre Lindenbaum

1 answer

I quickly wrote a tool to split a XML file: https://github.com/lindenb/jvarkit/wiki/Biostar165777

$  java -jar dist-1.139/biostar165777.jar -o out__SPLIT__.xml -T Hit -N 5 ~/blastn.xml

$ ls -la ~/blastn.xml out*.xml
-rw-rw-r-- 1 lindenb lindenb 422606 nov.  14 12:47 /home/lindenb/blastn.xml
-rw-rw-r-- 1 lindenb lindenb  86319 nov.  14 16:17 out001.xml
-rw-rw-r-- 1 lindenb lindenb  83570 nov.  14 16:17 out002.xml
-rw-rw-r-- 1 lindenb lindenb  85096 nov.  14 16:17 out003.xml
-rw-rw-r-- 1 lindenb lindenb  88297 nov.  14 16:17 out004.xml
-rw-rw-r-- 1 lindenb lindenb  87123 nov.  14 16:17 out005.xml

$  grep -cF "<Hit>" ~/blastn.xml out*.xml
/home/lindenb/blastn.xml:100
out001.xml:20
out002.xml:20
out003.xml:20
out004.xml:20
out005.xml:20
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updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

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