Chris, Having just encountered this need myself I think I have a way to do it. Its a little tricky but this will work. You need to make the protxml2html.pl program think that its being called by a web browser using a web server (or close enough). To do this you need to set two environment variables before running the command. Once they are set you don't have to set them again. So for the bash shell you would run:
export REQUEST_METHOD=GET export QUERY_STRING="sort=xpress_desc&min_prob=&show_groups=show&show_annot=show&show_peps=show&filter_xpress=yes&min_xpress=&max_xpress=&min_pep_prob=&min_ntt=&pep_aa=&mark_aa=&text1=&excel=yes&restore=no&exclusions=&inclusions=&pexclusions=&pinclusions=&xml_input=1&quant_light2heavy=true&coverage=&initial_probability=&xpress=&n_instances=&weight=&protlen=&group_number=&asapratio=&molweight=&prot_number=&num_tol_term=&peptide_group_designator=&libra=&protein=&peptide_sequence=&n_sibling_peptides_bin=&nsp_adjusted_probability=&annotation=&quant_light2heavy=true&num_unique_peps=show&tot_num_peps=show&xpress_display=show&asap_display=show" The first line sets the method of how parameters are passed to the program by the browser. The second (extremely long line) are all the parameters to pass. As you might guess you can modify/change them if you really wanted to -- though it is hard to read and might be easier just using Excel to do this. And if you are using csh instead of bash, you'd replace the "export REQUEST_METHOD=" with "setenv REQUEST_METHOD ". After running the two commands just then run the protxml2html program to get the xls file as so: protxml2html.pl -file *my.prot.xml file* EXCEL NOGAGGLE -Joe 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.
