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
>
> 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
>>
>> 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
>>>>>>
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>>>>>
>>>>
>>>>
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