Another tip: when using the "-C" option, the list of columns needs to include some sort of string formatting. For example, this is the full command I'm using to export:
~/ms_processing/tpp/cgi-bin/PepXMLViewer.cgi -C Gprotein,Gstart_scan,Gpeptide,Iiprobability,Gassumed_charge,Gcalc_neutral_pep_mass,Gprecursor_neutral_mass,Gmassdiff,Gprecursor_intensity,Gretention_time_sec,Gspectrum,Qlibra1,Qlibra2,Qlibra3,Qlibra4,Qlibra5,Qlibra6,Gppm,Gnum_missed_cleavages,Gions -B exportSpreadsheet 1 -I F01_ipro.pep.xml You can deduce the string formatting by holding the cursor over the "export to spreadsheet" button in tpp when viewing a pep.xml. Maybe someone with experience with C++ and or cgi scripting can explain the string formatting? -Adam On Monday, August 11, 2014 5:12:51 PM UTC-4, Adam Oberstein wrote: > > Dear TPP team, > > I'm trying to automate my data analysis workflow using the binaries > included with tpp v4.7.1 on linux. I have database search --> peptide > prophet --> iprophet working. I'd like to export the iprot.pep.xml data to > a spreadsheet file (.xls), as one would do manually in PepXMLViewer using > the "Other Actions --> Export Spreadsheet" option. > > Can someone advise me how I might go about doing this from the command > line or a script? > > Sincerely, > Adam Oberstein > Department of Molecular Biology > Princeton University > -- 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/d/optout.
