Chris, I have a couple of simple python scripts for generating CSV output from Pep or ProtXMLs. These should be relatively easy to modify to also output XPRESS ratios. You can find the code at https://github.com/jwinget/TPP_utilities if you'd like to try yourself. If I can find a ProtXML with the ratios in it, I'd be happy to take a stab at making the modifications.
Best, Jason On Sunday, May 26, 2013 11:41:56 AM UTC-7, chr12is wrote: > > Hi All, > > I seem to be having an issue with getting my output in excel format. I am > currently using TPP 4.6.2 on a linux cluster with CentOS. > > I generated my output.xml file using xinteract (running protein prophet as > part of this command). The resulting output.prot.xml file from xinteract > contains all the information I am interested in, including XPRESS ratios. > However, I now want to take my result file elsewhere to do some analysis, > such as R. To do this I would like to run some perl scripts on it, but > parsing an XML file with perl is a bit tedious. As such, I would like to > have it in Excel format so I can get the tab or comma delimited versions. > > I have tried to get the excel file using two options. This first is using > the 'protxml2html.pl' script and passing it the excel option. It seems > the XPRESS ratios are lost during this conversion. The html version doing > this also does not contain the XPRESS ratios. > > The second option is to re-run protein prophet on the resulting > interact.xml file and pass it the XPRESS option. It seems to work ok, but > when it gets to XPRESS, and says 'importing XPRESS ratios', it completes > almost instantly, and doesn't write the ratios to the file...otherwise the > file is ok. > > I am working on a cluster purely through command line, so a fix that is > based on this is desirable. > > Thanks for any suggestions you may have! > > Regards, > Chris > -- 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.
