Dear Scott, In case you had not managed to convert your results with tppXMLparser, you may have a try with RpepXML [*]. It is beta software and very much centred around Mascot pepXML result files, so I am not sure how it will behave with your data. If needed, I would be happy to debug and update the package to make it more generic.
Hope this helps. Best wishes, Laurent [*] http://rpepxml.r-forge.r-project.org/ -- Laurent Gatto slashhome.be On 11 September 2010 16:35, walmsls <[email protected]> wrote: > > 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. > > -- 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.
