The problem, I think, is that interProphet is filtering out all
analaysis_summary tags, when it really wants only to filter out the
peptideprophet ones (the CGI tips over when it can't find the ASAPRatio
summary).
Adding this at line 420 of InterProphetParser.cxx should solve the problem,
I think (but I'd like David to confirm):
else if (found && !strcmp(tag->getName(),
"analysis_summary")) {
// pass through any analysis summary that isn't
peptideprophet bpratt 5-27-09
if (tag->isStart() &&
strcmp(tag->getAttributeValue("analysis"),"peptideprophet")) {
output = !tag->isEnd(); // copy verbatim
until end tag is seen
tag->write(fout); // and copy the current
line
} else if (tag->isEnd()) {
output = false; // stop copying
}
}
- Brian
-----Original Message-----
From: [email protected]
[mailto:[email protected]] On Behalf Of Thomas
Sent: Thursday, May 28, 2009 5:32 AM
To: spctools-discuss
Subject: [spctools-discuss] Re: problem with ASAPcgi display and iprophet
Hi David,
I had some discussion with Brian off list. It seems like there are
some parts missing from the pepxml file
To continue here:
As a test I started the peptide prophet from the command line to
analyse 2 HPL runs from 1 independent experiments (in the end 8 HPLC
runs from 4 experiments):
C:\Inetpub\tpp-bin>xinteract -Nc:/Inetpub/wwwroot/ISB/data/Sabine/
Gruss/08-094u129TPP42r1/test_experiment/new_exp1_interact.pep.xml -
Eexp1 -p0.05 -l7 -Ol -X-m0.01-nK,6.0204-H-F35 -A-lK-F-r0.003 c:/
Inetpub/wwwroot/ISB/data/Sabine/Gruss/08-094u129TPP42r1/
test_experiment/08-094-04.pep.xml c:/Inetpub/wwwroot/ISB/data/Sabine/
Gruss/08-094u129TPP42r1/test_experiment/08-094-05.pep.xml
Afterwards I started iprophet from the gui:
run_in c:/Inetpub/wwwroot/ISB/data/Sabine/Gruss/08-094u129TPP42r1/
test_experiment; InterProphetParser c:/Inetpub/wwwroot/ISB/data/
Sabine/Gruss/08-094u129TPP42r1/test_experiment/
new_exp1_interact.pep.xml c:/Inetpub/wwwroot/ISB/data/Sabine/Gruss/
08-094u129TPP42r1/test_experiment/new_exp2_interact.pep.xml c:/Inetpub/
wwwroot/ISB/data/Sabine/Gruss/08-094u129TPP42r1/test_experiment/
new_exp3_interact.pep.xml c:/Inetpub/wwwroot/ISB/data/Sabine/Gruss/
08-094u129TPP42r1/test_experiment/new_exp4_interact.pep.xml
new_exp1234_interact.iproph.pep.xml
and finaly I started proteinprophet from the gui:
c:/Inetpub/wwwroot/ISB/data/Sabine/Gruss/08-094u129TPP42r1/
test_experiment/new_exp1234_interact.iproph.pep.xml c:/Inetpub/wwwroot/
ISB/data/Sabine/Gruss/08-094u129TPP42r1/test_experiment/
new_exp1234_iprophet_interact.prot.xml XPRESS ASAP_PROPHET
A folder (TPP-files ZMBH.zip) containing the following files is
uploaded:
one of the 8 mzML files
one of the 8 pep.xml after Mascot search (separate search with Mascot
daemon)
one of the 4 peptide prophet files interact.pep.xml
the .iproph.pep.xml
the interact.prot.xml with the iproph.pep.xml as input
Thanks,
Thomas
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