I wrote the pepXML viewer several years back. If you're comfortable doing it, you could certainly write your own parsing code using XSLT (blech) or use an xml parsing library in python, perl, etc. However, I found that there was enough domain-specifc information and some logic required to know how to interpret "what is important" in the XML file-- the schema doesn't fully specify all cases, and for example, a type of analysis may imply that certain other fields should appear. So I recommend using the viewer if possible, which takes these cases into account.
There are possibilities for faking a CGI environment so that you could run the viewer from the command-line; however, running it that way would basically take the same amount of time and memory. Your solution will probably depend on if you need to do this for a handful of files or hundreds. Please post back with any ideas or questions that I might be able to help you with. -Natalie On Wed, Sep 8, 2010 at 11:17 PM, walmsls <[email protected]> wrote: > Hi all: > Just wondering if there is a way to parse the pepxml (interact) file > that allows bypassing viewing the data in a web browser when exporting > to an xls (or tab delimited txt?) file? So far, viewing results in > explorer 64 bit is way quicker than opening the data set through a 32 > bit viewer, but is still a long wait (>2.5 gb memory dedicated to > opening the file in explorer). The intention is to analyze the > dataset with R code, with all of the data being vital to the analysis. > > Thank you in advance! > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
