Peter, a nice extra feature welcomed by myself would be to allow the optional inclusion of the Hit_defline in the output table. In many workflows we would need to blast, get the id from the table, use id to get human readible name and insert/use it.... which is silly of course since that data is available in the xml anyway. I don't know python and about hg changesets but I modified your python and xml file to incorporate this (see attachement). By default its normal blast tabular output but optionally it can include the defline. The hit_defline needed to be split (I hope I did it in a python way) to eliminate multiple discriptions separated by >gi (nt and nr) or plain semicolons for swissprot.... maybe there are more but not sure... Have a look and test and maybe it will find the way in some form into your suite. Anyway its very useful in this way to us. cheers Alex ________________________________________ Van: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] namens Bossers, Alex [Alex.Bossers@wur.nl] Verzonden: woensdag 24 november 2010 22:18 Aan: peter@maubp.freeserve.co.uk CC: Galaxy Dev Onderwerp: Re: [galaxy-dev] blastxml to tabular bug fix Peter green box for me :) Works like a charm. hanks for the rapid fix. Alex ________________________________________ Van: p.j.a.cock@googlemail.com [p.j.a.cock@googlemail.com] namens Peter [peter@maubp.freeserve.co.uk] Verzonden: woensdag 24 november 2010 16:13 Aan: Kanwei Li CC: Bossers, Alex; Galaxy Dev Onderwerp: blastxml to tabular bug fix Hi Kanwei, Could you check and commit the following three changesets from my new branch: http://bitbucket.org/peterjc/galaxy-central/src/blastplus_nov24 i.e. these three changesets: http://bitbucket.org/peterjc/galaxy-central/changeset/8f0e5a169630 http://bitbucket.org/peterjc/galaxy-central/changeset/72fab21f9469 http://bitbucket.org/peterjc/galaxy-central/changeset/72fab21f9469 This address a problem found earlier today by Alex Bossers (CC'd) while testing the BLAST+ wrappers. The problem can occur when when the query sequence is masked (with XXXX characters), this broke my calculation of the identity and mismatch counts (failing an assert statement I'd included as a sanity check). The new unit test is a cut down version of his failing example. Note that in order to run the unit tests, you will need to first re-enable the tool in tools_conf.xml.sample - the converter tests does not depend on the BLAST+ binaries being installed. Thank you, Peter _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev