Hi, I'm looking for simple way of converting blast output in text (stardard output) into XML format (maybe some has got script?). I've looked elsewhere but couldn't find anything:/
UPDATE
I ended up running blastall with -m7, but stil someone may benefit from BlastConverter :)
5 answers
did you know that the 'blastall' command line has an option (-m 7) for generating an XML output ? http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastall/blastall_node29.html
If you're using the web interface of the NCBI for blast, the result can be downloaded as XML (or ASN1,... )
most Bio* packages can parse blast (e.g. http://www.bioperl.org/Core/Latest/bptutorial.html#iii_4_2_parsing_blast_and_fasta_reports_with_search_and_searchio ) but I don't know if there is a predefined method to export the data as XML.
I to have this problem. Which cannot be solved by re-running blast. I am currently writing a script to do it as I cannot find any solutions online. It's slightly annoying that the default text/html output seems to be the least amenable to conversion. If I come up with anything useful I'll make sure it is made available.
Extremely simple task:
<xml>
<blast>
<![CDATA[
copy your blast result here.
]]>
</blast>
</xml>
Easy way for valid xml when no XML Schema is specified :P
•
written
by
Anon1234Y •
For a script to convert the default NCBI BLAST text output (as specified with '-outfmt 0' for NCBI BLAST+ or '-m 0' for legacy NCBI BLAST) into NCBI BLAST XML, see the following thread in the Blast2GO Google Group:
https://groups.google.com/forum/#!topic/blast2go/zJJCN-timCg
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Please add some example output... Why do you want it as XML anyway?
I would be interested in a solution to this as well. My BLAST+ run is eating all 64GB of my RAM in BLASTXML format. I have to have BLASTXML format to support MEGAN, but if I can convert a standard run to BLASTXML that would be ideal--assuming it stores data less verbosely in RAM.