Hi Brian, Thanks for the quick reply - this fix does solve the search results file name issue but now there are problems with viewing the spectra (using pepXML viewer) which lead to Windows error message saying: "plot-msms.cgi has encountered a problem and needs to close. We are sorry for the inconvenience." etc. In the Apache error log I case see the following line if that might help somehow: "[Tue Mar 03 11:16:28 2009] [error] [client 127.0.0.1] Use of uninitialized value in -d at C:/Perl/lib/CGI.pm line 4083., referer: http://localhost/tpp-bin/tpp_gui.pl?Action=display&page=results [Tue Mar 03 11:16:52 2009] [error] [client 127.0.0.1] Premature end of script headers: plot-msms.cgi, referer: http://localhost/ISB/data/OK1/June07/interact.pep.shtml Cheers, Oded
On Mar 2, 9:43 pm, "Brian Pratt" <brian.pr...@insilicos.com> wrote: > Oded, > > I'm sure you're right in your diagnosis, and thanks for doing the hard part! > > Try changing this line > $out_file =~ s/\.mz[X]?ML$/\.tandem/i; > to > $out_file =~ s/\.mz[X]?ML(\.gz)?$/\.tandem/i; > > Please let me know if that works and I'll make the change for the next > release. > > Thanks, > > Brian > > -----Original Message----- > From: spctools-discuss@googlegroups.com > > [mailto:spctools-disc...@googlegroups.com] On Behalf Of Oded > Sent: Saturday, February 28, 2009 11:33 AM > To: spctools-discuss > Subject: [spctools-discuss] Error using mzXML.gz as input > > Hi all, I'm having problems using the gzipped mzXML files as input (In > TPP 4.2 both on OS X and Win). > While doing X!Tandem search the results file overwrite the input file > and appear > under that same name without the ".tandem" > For example the search results of Seq1.mzXML.gz will have the > name of "Seq1.mzXML.gz" and not the name "Seq1.tandem" > or something similar. (look like similar to what happened in 4.1 rev > while using mzXL > see:http://groups.google.com/group/spctools-discuss/browse_thread/thread/63b > 8a308c04aaf3d/1cadb91f3ac730b5?lnk=gst&q=mzml#1cadb91f3ac730b5 so I guess it > shouldn't be too hard to > fix) > > Cheers, > Oded --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
