blastxml

[Wenlan Tian]

Hi,all,
I had done a blastall search and got a xml output file. How could i parse
it to other format? I've found many scripts online, but no one worked. I am
new to linux. Can anyone give me a good script to use?

Thanks,
Vivi
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[Peter Cock]

On Monday, April 29, 2013, Wenlan Tian wrote:

Hi,all,
I had done a blastall search and got a xml output file. How could i parse
it to other format? I've found many scripts online, but no one worked. I am
new to linux. Can anyone give me a good script to use?

Thanks,
Vivi

Hi Vivi,

What format are you trying to convert the BLAST XML into?

Have you looked at BioPerl's SearchIO module?

http://www.bioperl.org/wiki/HOWTO:SearchIO

If you also know Python, I'd suggest trying Biopython's new

experimental SearchIO module which would let you convert

BLAST XML to tabular for example:

http://biopython.org/wiki/SearchIO

Or my older standalone Python script to do that

(which comes with a Galaxy wrapper), see:

https://bitbucket.org/peterjc/galaxy-central/src/tools/tools/ncbi_blast_plus/blastxml_to_tabular.py?at=tools

Peter

[Smithies, Russell]

There are several options depending on how much data you have:
1) re-run the blast searches using a more appropriate output format
2) use the BioPerl SearchIO module with option -format=>'blastxml'
3) use an XSLT to transform your xml to a tabular format
4) use simple grep, sed, and awk commands to extract the bits you want

--Russell

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