Only if "*.pep.xml" accidentally picks up something you didn't mean it to - like maybe an interact.pep.xml file from a previous run.
-----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Kristian Sent: Thursday, April 23, 2009 12:12 PM To: spctools-discuss Subject: [spctools-discuss] Re: Limit on number of pep.xml files that can be analyzed with XInteract? There it goes. Is there any difference in the analysis or output with or without globbing? On Apr 23, 12:09 pm, "Brian Pratt" <[email protected]> wrote: > On windows those need to be double quotes, "*.pep.xml". > > > > -----Original Message----- > From: [email protected] > > [mailto:[email protected]] On Behalf Of Kristian > Sent: Thursday, April 23, 2009 12:05 PM > To: spctools-discuss > Subject: [spctools-discuss] Re: Limit on number of pep.xml files that can be > analyzed with XInteract? > > The globbing command doesn't seem to work for me. > > When I enter the command > > >xinteract '*.pep.xml' > > the command line returns > > error, cannot parse input file '*.pep.xml' > > However, the command > > >xinteract *.pep.xml > > works with 120 input files. > > On Apr 23, 11:21 am, Luis Mendoza <[email protected]> wrote: > > Hi Chris, > > Did you try: > > > xinteract '*.pep.xml' -Ninteract.pep.xml -p0.05 -l9 -OAp > > -X-m0.15-nR,10-nK,8-L > > > (note the quotes around the input file 'glob'). > > --Luis > > > On Thu, Apr 23, 2009 at 10:08 AM, Chris Hughes <[email protected]> > wrote: > > > > I am having trouble getting this to work. I have 170 files in a > > > directory. > > > > If I navigate to the directory in command prompt and type: xinteract > > > *pep.xml it will go through all my files in terminal, but then at the > > > end there will be a --L"7"" exited with the non-zero exit code: 1 QUIT > > > - The job is incomplete > > > > Is there something I am doing wrong here? Ideally the command I would > > > like to run on all my files is: > > > > xinteract -Ninteract.pep.xml -p0.05 -l9 -OAp -X-m0.15-nR,10-nK,8-L > > > > Thanks! > > > > Chris > > > > On Apr 22, 3:18 pm, Luis Mendoza <[email protected]> wrote: > > > > Hello Kristian, > > > > Glad you were able to complete your analysis. One potential thing to > > > watch > > > > out for when you use wildcards (i.e. the asterisk) is that you may > > > > inadvertently include a file that you did not mean to, for example: an > > > old > > > > analysis file with the name interact-old.pep.xml ; this would > naturally > > > > affect your results. > > > > > As of now, there is no simple way to have Petunia get past the shell > > > limit > > > > on number of files/characters. Perhaps we could add an "Analyze all > > > pep.xml > > > > files in this directory" button or some such. Although in general I > > > would > > > > suggest using a command-line or even a script if you will be running > > > > analyses on very large numbers of files. > > > > Cheers, > > > > --Luis > > > > > On Wed, Apr 22, 2009 at 12:00 PM, Kristian < > > > [email protected]>wrote: > > > > > > Answered my own question. I was able to run the commands from > Windows > > > > > command line. > > > > > > the command >xinteract *.pep.xml analyzed all 120 of my .pep.xml > > > > > files. > > > > > > I copied the command line from the petunia window to incorporate my > > > > > ICAT ratios and run protein prophet after: > > > > > >xinteract -Ndesiredfilename.pep.xml -p0.05 -l7 -Oip -X-m1.0-L > > > -A-lC-r0.5 > > > > > *.pep.xml > > > > > > On Apr 22, 10:13 am, Kristian <[email protected]> wrote: > > > > > > I use petunia on a Windows machine, so there is no command line > from > > > > > > my end. I use the default settings. I'm not even sure what > Eric's > > > > > > post means. > > > > > > Is there a line I can edit in one of the GUI files to get around > this > > > > > > limitation? Or otherwise, can I enter the commands in the Windows > > > > > > command line and get around it? > > > > > > > On Apr 21, 4:26 pm, "Eric Deutsch" <[email protected]> > > > > > > wrote: > > > > > > > > It is likely the shell that imposes the limit. > > > > > > > > When you type: > > > > > > > > xinteract *.pep.xml > > > > > > > > the shell expands that wildcard into the full list before > feeding > > > the > > > > > list > > > > > > > to xinteract. The shell has an inherent limit. xinteract does > not. > > > For > > > > > this > > > > > > > very reason, you can get xinteract to the globbing for you with: > > > > > > > > xinteract '*.pep.xml' > > > > > > > > This causes the wildcard to be passed to xinteract and it will > > > resolve > > > > > it > > > > > > > for you. This has been used on over 35,000 pepXML files at once. > It > > > > > works. > > > > > > > > Eric > > > > > > > > > -----Original Message----- > > > > > > > > From: [email protected] [mailto:spctools- > > > > > > > > [email protected]] On Behalf Of Brian Pratt > > > > > > > > Sent: Tuesday, April 21, 2009 4:11 PM > > > > > > > > To: [email protected] > > > > > > > > Subject: [spctools-discuss] Re: Limit on number of pep.xml > files > > > that > > > > > can > > > > > > > > be analyzed with XInteract? > > > > > > > > > There's not meant to be a limitation - can you give an example > of > > > a > > > > > > > > command > > > > > > > > line that fails? > > > > > > > > > -----Original Message----- > > > > > > > > From: [email protected] > > > > > > > > [mailto:[email protected]] On Behalf Of > Kristian > > > > > > > > Sent: Tuesday, April 21, 2009 3:00 PM > > > > > > > > To: spctools-discuss > > > > > > > > Subject: [spctools-discuss] Re: Limit on number of pep.xml > files > > > that > > > > > can > > > > > > > > be > > > > > > > > analyzed with XInteract? > > > > > > > > > I have installed 4.2.1, but the problem persists. After a bit > of > > > > > > > > experimenting, I've found that XInteract can only handle up to > 99 > > > > > > > > input *.pep.xml files at a time. > > > > > > > > > The operation fails with the message "failed: Operation not > > > > > > > > permitted". > > > > > > > > > On Apr 16, 1:21 pm, Natalie Tasman > <[email protected]> > > > > > wrote: > > > > > > > > > Hi Kristian, > > > > > > > > > > Also, 4.2.1 contained many bug fixes. I'm not sure if this > > > would > > > > > have > > > > > > > > been > > > > > > > > > addressed, but it's always most efficient for us if you can > try > > > to > > > > > > > > replicate > > > > > > > > > the issue on the latest version. > > > > > > > > > > -Natalie > > > > > > > > > > On Thu, Apr 16, 2009 at 12:42 PM, Christine Vogel > > > > > > > > <[email protected]>wrote: > > > > > > > > > > > I have had some problems before if any of the pep.xml > files > > > had > > > > > > > > identical > > > > > > > > > > names. Renaming them (and paths/names within the files) > > > solved > > > > > that > > > > > > > > > > problem. > > > > > > > > > > > Christine > > > > > > > > > > > On Thu, Apr 16, 2009 at 2:17 PM, Brian Pratt > > > > > > > > <[email protected]>wrote: > > > > > > > > > > >> There's not meant to be a limitation - can you give an > > > example > > > > > of a > > > > > > > > > >> command > > > > > > > > > >> line that fails? > > > > > > > > > > >> -----Original Message----- > > > > > > > > > >> From: [email protected] > > > > > > > > > >> [mailto:[email protected]] On Behalf Of > > > > > Kristian > > > > > > > > > >> Sent: Thursday, April 16, 2009 11:56 AM > > > > > > > > > >> To: spctools-discuss > > > > > > > > > >> Subject: [spctools-discuss] Limit on number of pep.xml > files > > > > > that can > > > > > > > > be > > > > > > > > > >> analyzed with XInteract? > > > > > > > > > > >> I'm using TPP 4.2.0 to analyze cleavable ICAT data from > an > > > LCQ. > > > > > When > > > > > > > > > >> all replicates are done, I have 120 seperate .pep.xml > files > > > to > > > > > > > > combine > > > > > > > > > >> and analyze. With earlier versions of TPP (i.e. 3.4) I > > > could > > > > > analyze > > > > > > > > > >> them all at once with Xinteract, but with 4.2 the > operation > > > > > simply > > > > > > > > > >> aborts and fails with no error message. I can analyze > the > > > files > > > > > 40 > > > > > > > > at > > > > > > > > > >> a time and then combine the interact.pep files in protein > > > > > prophet, > > > > > > > > but > > > > > > > > > >> I'm curious if and why there's a limitation on the number > of > > > > > input > > > > > > > > > >> files for Xinteract.- Hide quoted text - > > > > > > > > > > - Show quoted text -- Hide quoted text - > > > > > > > > - Show quoted text -- Hide quoted text - > > > > > > > - Show quoted text -- Hide quoted text - > > > - Show quoted text -- Hide quoted text - > > - Show quoted text - --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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