Question: Blast Text-Output To Xml Converter
2
gravatar for Leszek
8.6 years ago by
Leszek4.0k
IIMCB, Poland
Leszek4.0k wrote:

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 :)

xml blast conversion • 7.8k views
ADD COMMENTlink modified 2.2 years ago by Biostar ♦♦ 20 • written 8.6 years ago by Leszek4.0k

Please add some example output... Why do you want it as XML anyway?

ADD REPLYlink written 8.6 years ago by Egon Willighagen5.2k

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.

ADD REPLYlink written 8.6 years ago by Lythimus200
5
gravatar for Pierre Lindenbaum
8.6 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum121k wrote:

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.

ADD COMMENTlink modified 8.6 years ago • written 8.6 years ago by Pierre Lindenbaum121k

I'm aware of that, however I would love to use blast-machine for computation (DeCypher by Timelogic) and it doesn't give xml output, only ncbi like text output... So this is why I'm asking...

ADD REPLYlink written 8.5 years ago by Leszek4.0k
2
gravatar for Darked89
8.6 years ago by
Darked894.2k
Barcelona, Spain
Darked894.2k wrote:

blastall already has an option of producing XML:

blastall -m 7

Simply rerun your blast search instead of writing a parser.

ADD COMMENTlink written 8.6 years ago by Darked894.2k

I have the feeling the submitter might not have the possibility to (re-)run that BLAST.

ADD REPLYlink written 8.6 years ago by Bach550

I would love to use blastall, however running regular blast will take ages... I need to do it on blast-machine and feed xml-formatted output to another step:/

ADD REPLYlink written 8.5 years ago by Leszek4.0k
0
gravatar for Dwood
8.6 years ago by
Dwood0
Dwood0 wrote:

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.

ADD COMMENTlink written 8.6 years ago by Dwood0
0
gravatar for Anon1234Y
8.6 years ago by
Anon1234Y10
Anon1234Y10 wrote:

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

ADD COMMENTlink written 8.6 years ago by Anon1234Y10

this is not going to solve the problem at all

ADD REPLYlink written 8.5 years ago by Leszek4.0k
0
gravatar for Hamish
5.8 years ago by
Hamish3.1k
UK
Hamish3.1k wrote:

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

ADD COMMENTlink written 5.8 years ago by Hamish3.1k
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