ProteinProphet XSLT viewing problems

[sirlark]

Hi,

Firstly, I'm using TPP v4.5 RAPTURE rev 2, Build 201202071404 (linux)

I've tried running protein prophet three different ways, with different results. 

The first way, I analyse peptides without choosing to run interprophet. Then I run proteinprophet on the interact.pep.xml file. It runs fine, no complaints. But when I try to view the file, I get this error:

Error loading stylesheet: Parsing an XSLT stylesheet failed.

The second way, I analyze peptides without choosing to run interprophet. Then I run interprophet on the single interact.pep.xml file, and then proteinprophet on the interact.iproph.pep.xml, marking "input is from Iprophet". Again, viewing the results I get 

Error loading stylesheet: Parsing an XSLT stylesheet failed.

The third way is the same as the second way excpet I also check "pregenerate html file" (in the hopes of bypassing the XSLT error. During the run I see the following output, and 

[Mon Jun 25 14:06:19 2012] EXECUTING: /usr/local/tpp/bin/protxml2html.pl -file /usr/local/tpp/data/ValidationSet/0000/interact.prot.xml HTML 
OUTPUT:
Writing results to html file: /usr/local/tpp/data/ValidationSet/0000/interact.prot.html
runtime error: file /usr/local/tpp/data/ValidationSet/0000/interact.prot.xsl line 197 element param
Unexpected XSLT element 'param'.
runtime error: file /usr/local/tpp/data/ValidationSet/0000/interact.prot.xsl line 197 element A
Variable 'mypep' has not been declared.
xmlXPathCompiledEval: evaluation failed
Done!
END OUTPUT

View interact.pep.xml gives the same XSLT error, and viewing the interact.pep.html shows truncated output for a single protein.

If I log in to the TPP server and view the interact.pep.xml files using less/cat, all the info seems to be there.

Thanks,
James

[Brian Hampton]

Hello James,

When this happened to me it turned out to be an Apache problem.  My install of Apache2 didn't have SSI includes enabled.  Luis pointed me in the right direction to find that out...  Below is my reply to the list when I got it working.  I hope yours is as easy to fix.

Cheers,

Brian

Hi Luis,

Thanks so much for your help.  Indeed the Apache2 default install conveniently does not have SSI includes enabled.  A simple a2enmod include and a restart of apache did the trick.

Thanks for the tip.  I can now use the complete TPP on a data set and actually see the results!

Thanks,

Brian Hampton

[sirlark]

Hi Brian,

Thanks for the swift reply. I remember seeing the SSI thread before. I tried it, and Interprophet suddenly started seg faulting. Turns out it was something else i did around the same time, but I never got around to re-enabling the SSI includes. I have done so now, and I can view .shtml links, but I'm still getting the runtime errors when running InterProphet, and I still only see 1 truncated protein's output.

Thanks,
James

[Luis Mendoza]

Hi James,
Do you know what xsl processor you are using on your system? It may
well be that our generated xsl is incompatible with it (we use
xsltproc). Can you try using a different one and see what happens?
Cheers,
--Luis

> --
> You received this message because you are subscribed to the Google Groups
> "spctools-discuss" group.
> To view this discussion on the web visit
> https://groups.google.com/d/msg/spctools-discuss/-/2keL64Ect8sJ.
>
> To post to this group, send email to spctools...@googlegroups.com.
> To unsubscribe from this group, send email to
> spctools-discu...@googlegroups.com.
> For more options, visit this group at
> http://groups.google.com/group/spctools-discuss?hl=en.

[sirlark]

Hi Luis,

I'm not sure which xsl processor I'm using. TPP is running on an Ubuntu server lucid system. How do I find out which xsl proccessor is used and how would I get TPP to use a different one?

[Brian Hampton]

Hi Luis and James,

I have the same problem.  When viewing any iproph interact file the viewer only shows the first protein in the list and cuts off at the first peptide in the display listing.  However, I can export the data as an excel spreadsheet and all the data is there.  So it is definitely related to displaying the interact.iproph.xml file.

Luis, we are using xsltproc.  

Thanks for any help/advice!

Brian