I just committed the change. Please update from trunk, recompile
PeptideProphetParser and try it again.
Thanks,
-David
On Wed, Nov 10, 2010 at 2:12 PM, ira cooke wrote:
> Hi David,
> Thanks very much for fixing this. Would you recommend that we check
> out the latest source and just recompile
Hi David,
Thanks very much for fixing this. Would you recommend that we check
out the latest source and just recompile PeptideProphet? I guess this
would be safer than upgrading our whole TPP install to the latest
code?
We'll contact Phenyx support about the pepXML dump and hopefully they
can fi
Hello again,
I realized you sent me the db and each protein listed only once, so
the problem is with the Phenyx pepXML dumper writing these incorrect
tags. Temporarily, I have removed these entries using the sed
command: sed -i 's/^http://groups.google.com/group/spctools-discuss/web/interact.pep.
Hi Ira,
Thanks for providing your Phenyx search results. I was able to
resolve a bug in PeptideProphet, which was preventing it from reading
in any Phenyx search results. At this point I still cannot process
these files with PeptideProphet because of the alternative_protein
entries. Somehow, th
Hi David,
I've uploaded the database and original file .. the file is called
iracooke_phenyx_pepXML.tar.gz
The files I've uploaded are all unmodified output from the search
(performed on a different machine to where the TPP is installed). I'd
previously tried changing some of the paths in the file
It would be helpful to see all of the output from the latest command.
You might have to unravel the pipeline and run the steps separately if
the Phenyx pepXML is missing some information. Would it be possible
for you post you Phenyx pepXML file and the database so I can try it
in a debugger?
Than
Thanks for your quick response.
I've modified my command to
/usr/local/tpp-4-4-0/bin/xinteract -Ninteract.pep.xml -p0 -eT -l7 -D/
var/www/ISB/data/Databases/OnMascot/SPHuman/
sphuman_20101013_DECOY.fasta -OdP -ddecoy 206_pepxml.xml
(also tried without the -Od option).
Unfortunately I still get
