Hi Robert,
As you may have noticed, we have been phasing out the old protXML viewer
(and associated helper scripts) in favor of a new, faster, and more modern
one. We have implemented the majority of the old functionality into the
new one (and much more!), so we have decided to retire the old one as of
the last release.
The new viewer is able to generate a tab-delimited file from a protXML
document. You can get a usage statement by typing its name on the command
line:
%> ./tpp/cgi-bin/ProtXMLViewer.pl
I need an input file!
-------------------------------------------------------------------------
ProtXML Viewer (TPP v5.1.0 Syzygy, Build 201711031424-exported
(Linux-x86_64))
Command-line usage:
./tpp/cgi-bin/ProtXMLViewer.pl -file <full_path_to_protXML_file> -action
<action> [options]
values for <action> are: ExportExcel or ExportDat
Options:
-peps export one peptide per line for ExportExcel [default:
export one protein per line, with all peptides in one column]
-fx <field> name of field to export [required for ExportDat]
-fy <field> name of second field for 2-column export [optional]
values for <field> are: Probability, Coverage, Pct_Spectrum_ids,
Num_Peptides, Xpress_Npeps, ASAP_Npeps,
Libra_Npeps, Xpress_Heavy, ASAP_Heavy,
ASAP_pvalue, StPeter_Quant
Exiting.
To generate a file with the same format as the old viewer:
%> ./tpp/cgi-bin/ProtXMLViewer.pl -file /users/data/test/interact.prot.xml
-action ExportExcel -peps
Apologies for the late reply, and hope this helps!
--Luis
On Mon, Nov 5, 2018 at 10:41 PM, Robert <robert.wink...@bioprocess.org>
wrote:
> Hi, I just run the TPP docker Prophet scripts.
> However, the EXCELxx option for exporting the protein results into a
> tabular format seems not to work (in contrast, EXCELPEPS works).
> I also tried perl propxml2html.pl, but it complains: pepxml2html.pl:
> cannot open xsl file : No such file or directory.
> Is there any (standard) way on how to get the prot.xml into a tabular text
> format with the tpp docker image?
> Best, Robetr
>
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