Thanks Natalie and Brian for your input. I do have CPAS for a long time, not quite sure why i never thought of importing data into the pipeline!
Funny thing, I ran across this other program a while back and left it on my pc and forgot about it. Here's a weblink to a program called tppxmlparser.jar written by Dr. Damian Fermin at U. Michigan: damianfermin.com/software.html >>scroll down to tppxmlparser.jar The program outputs common, but not all tags in the pepxml (and protxml) files. It includes a sql connector to populate tables. I wrote Damian for instruction on how to alter source to get specific output I may be interested in from the pepxml and it seems easy enough. Scott On Sep 10, 3:57 pm, Brian <[email protected]> wrote: > Another option might be to use CPAS, which is part of the LabKey > server (seehttps://www.labkey.org/wiki/home/Documentation/page.view?name=ms2). > > You could import your pepXML files into CPAS and then use the RLabkey > (http://cran.r-project.org/web/packages/Rlabkey/index.html) R package > to connect to CPAS and slurp the data into an R data frame. You can > query either a single file or many files and perform comparisons. > More information on the using the RLabkey package with CPAS is > available athttps://www.labkey.org/wiki/home/Documentation/page.view?name=rAPI > > This solution will probably be overkill if you only need to do this > for a handful of files, but if you have hundreds it might be worth > taking a look at. > > -Brian > > On Sep 9, 10:09 am, Natalie Tasman <[email protected]> > wrote: > > > 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 > > > athttp://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.
