Continuing on this theme, I finally found the code describing the commmand
line options for PepXMLViewer.cgi in the c++ source code file
/tpp_4.7.1/src/Visualization/PepXMLViewer/PepXOptions.cxx.
Line 823 has the comment: "// TODO: print usage"
..yes, that would've been nice.
Here is a short summary which may be useful to others:
Usage: /path_to_tpp_install_dir/tpp/cgi/PepXMLViewer.cgi [OPTIONS...] -I
file.pep.xml
Options summary:
-I {xml file name}
-P {per page} #probably not relevant for command line
-p {page} #probably not relevant for command line
-C {columns; comma separated string} #this will allow election of columns
and order during spreadsheet export
-S {sort field; defaults to "prob"}
-X {exclude charge state; integer}
-F {filter} #not sure how this works, but likely to be described in the
same file
-B {boolean taking one of the following options followed by 1 or 0 to
indicate True or False}
"requireGlyc"
"includeBinGlycMotif"
"requireIonscoreGTidentityscore"
"requireIonscoreGThomologyscore"
"requireASAP"
"requireXPRESS"
"requireASAPConsistent"
"lowToHighASAP"
"expandProteinList"
"exportSpreadsheet"
"minimizeTableHeaders"
"includeHighlightedPepTextMods"
"includeRequiredPepTextMods"
***Note: "exportSpreadsheet" is obviously useful with regard to this thread
-R {various filtering options, seems to be most useful for tpp_gui since
this can be done easily once the data is exported to spreadsheet file. See
PepXOptions.cxx lines 959-1018 if interested}
--Adam
On Friday, August 15, 2014 12:36:51 PM UTC-4, Adam Oberstein wrote:
>
> Thanks Jason,
>
> I think I can use or modify your scripts for my purpose.
>
> Best,
> Adam
>
> On Friday, August 15, 2014 12:32:16 PM UTC-4, Jason Winget wrote:
>>
>> This is a question that comes up fairly often. The command-line Luis
>> posted works, but I've also created some simple-to-use python scrips to
>> export either PepXML or ProtXML to comma-separated variable format.
>> You can get them here: https://github.com/jwinget/TPP_utilities
>>
>
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