Christine, Thanks for pointing this out and I'm glad to say this change is already in the trunk. Back in April I spent a little time running the pepxml files TPP produces through a XML validator to ensure that what we produced was valid XML and matched the pepXML schema. Needless to say we had to make a few adjustments to both the standard and the code and this was one of those changes. It'll be going out in the 4.6.3 release which should be announced very soon.
-Joe On Thu, Jun 27, 2013 at 5:25 PM, Christine <[email protected]>wrote: > Thanks Dave. This works! > > So as the script is not exactly as it was in 2009, I moved the line from > line 4546 to line 4545 (protxml2html.pl, v4.6.2): > print XSL '<xsl:param name="mypep"/>'; > > That means this line should be before (instead of after): > print XSL '<xsl:variable name="PepMass"><xsl:if > test="@calc_neutral_pep_mass"><xsl:value-of > select="@calc_neutral_pep_mass"/></xsl:if></xsl:variable>'; > > > Cheers, > Christine > > > Le vendredi 28 juin 2013 08:03:03 UTC+10, Dave Trudgian a écrit : > >> Ahh, the fix back then was this: >> >> https://groups.google.com/**forum/#!searchin/spctools-** >> discuss/xslt/spctools-discuss/**0h73qbqbqes/CFRakqDIQeAJ<https://groups.google.com/forum/#!searchin/spctools-discuss/xslt/spctools-discuss/0h73qbqbqes/CFRakqDIQeAJ> >> >> Probably more important was that I now remember that running the xslt >> translation through Xalan (rather than xsltproc) gave a nice error message >> that indicated exactly what the problem was. Maybe that'd work this time? >> Happy to look if anyone wants to send me a .prot.xml file. >> >> DT >> >> >> On Thursday, June 27, 2013 4:59:25 PM UTC-5, Dave Trudgian wrote: >>> >>> This is the same outcome I had with a problem in 4.2.0 back in 2009: >>> >>> https://groups.google.com/**forum/#!searchin/spctools-** >>> discuss/xsltproc/spctools-**discuss/47vHn08zLjU/**7amlOxqjrCoJ<https://groups.google.com/forum/#!searchin/spctools-discuss/xsltproc/spctools-discuss/47vHn08zLjU/7amlOxqjrCoJ> >>> >>> Maybe the problem, and fix is similar - I remember modifying the code to >>> make it work, but don't have it handy to check back what I did. Don't have >>> a 4.6.2 installation to check either. I will try to find out what I did... >>> >>> On Monday, June 24, 2013 8:52:33 PM UTC-5, Christine wrote: >>>> >>>> Hi Luis, >>>> >>>> Thanks for your answer. Pls find attached 2 screenshots (default view, >>>> only the 1st protein hit; and when "peptides hide" is checked, all protein >>>> hits) and web server error.log >>>> Let me know if you need something else. >>>> >>>> Regards, >>>> >>>> Christine >>>> >>>> >>>> >>>> Le mardi 25 juin 2013 11:33:27 UTC+10, Luis a écrit : >>>>> >>>>> Hello everyone, >>>>> Can you send us a couple of screenshots so we can see what you mean by >>>>> "only display the first protein hit"? I have not been able to >>>>> replicate this in Windows or Linux. >>>>> Thanks, >>>>> --Luis >>>>> >>>>> >>>>> >>>>> On Mon, Jun 24, 2013 at 6:26 PM, <[email protected]> wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> same problem here with TPP4.6.2. Has anybody solved this? >>>>>> >>>>>> Thanks, >>>>>> Christine >>>>>> >>>>>> Le vendredi 15 février 2013 06:42:49 UTC+10, Brian Hampton a écrit : >>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> Using a Ubuntu install of TPP4.6.1 the ProtXML viewer will only >>>>>>> display the first protein hit from an iProphet result. However, I >>>>>>> discovered today that if I check "hide" for peptides, then it displays >>>>>>> the >>>>>>> entire result set. It will export to Excel the results with any >>>>>>> setting. >>>>>>> >>>>>>> Maybe this clue will help troubleshoot for a solution.. >>>>>>> >>>>>>> Thanks in advance, >>>>>>> >>>>>>> Brian >>>>>>> >>>>>> -- >>>>>> You received this message because you are subscribed to the Google >>>>>> Groups "spctools-discuss" group. >>>>>> To unsubscribe from this group and stop receiving emails from it, >>>>>> send an email to spctools-discu...@**googlegroups.com. >>>>>> To post to this group, send email to [email protected]. >>>>>> Visit this group at >>>>>> http://groups.google.com/**group/spctools-discuss<http://groups.google.com/group/spctools-discuss> >>>>>> . >>>>>> >>>>>> For more options, visit >>>>>> https://groups.google.com/**groups/opt_out<https://groups.google.com/groups/opt_out> >>>>>> . >>>>>> >>>>>> >>>>>> >>>>> >>>>> -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/groups/opt_out. > > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/groups/opt_out.
