On Fri, Jan 17, 2014 at 8:34 AM, Bossers, Alex <alex.bossers@wur.nl> wrote:
Peter, We will definitely give them a try.
Great.
I never understood why the tabular outputs did have an option to include the defline/hit decryption.
That was a long standing gripe of mine too, fixed in BLAST+ 2.2.28 and available in the BLAST+ wrappers on the main Tool Shed since Dec 2013, http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/ - see also: http://blastedbio.blogspot.co.uk/2012/05/blast-tabular-missing-descriptions....
Just for that we needed to use the cloggy XML output and parse that into a table again.
Yes, that was a pain. It was the main reason for writing this tool: http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
Conserved header names are more useful to us than having column numbers. But either is fine with us. Alex
Yes, I'd also like the standard BLAST+ tabular output to include a # (hash) commented header line listing the fields (tab separated). They do something like this in the extremely verbose commend tabular output, but that adds a lot of other largely redundant comment lines as well :( Regards, Peter