Merging Blast results - xml or tabular format

[mstagliamonte]

Hi, everybody,

I have broken a large fasta file into smaller ones, and run parallel BLAST queries on multiple processors. I was thinking to merge the output files with cat - but I later realised that .xml files merging may not be such a trivial task. Have you got any suggestions?
I chose the xml because I could feed them to Megan and convert them to tabular to also use them for Galaxy

Would you suggest me to run the next queries asking for tabular format (running MEGAN was more of a curiosity than a necessity)? Would it be correct to merge tabular just with cat command?

Thanks for your help
Max

[rhinoceros]

Yes, you can merge tabular with cat and further still, you can feed that into MEGAN too. I don't know about merging the xml output..

[maubp]

I wrote some code to merge BLAST XML files as part of supporting them within Galaxy, that Python code is now here: https://github.com/peterjc/galaxy_bl...types/blast.py

See also http://www.biostars.org/p/53946/

The basic idea is you need a single XML header and footer - simple concatenation repeats this and you don't get a valid XML file.

[mstagliamonte]

Thanks, to the both of you

I know a bit of Python, but I wasn't sure why the cat command would not generate valid files. that is really interesting, good to know for the future.
I will review MEGAN manual as well, I must have missed the tabular as possible input


Kind Regards,
Max