There it goes. Is there any difference in the analysis or output with or without globbing?
On Apr 23, 12:09 pm, "Brian Pratt" <brian.pr...@insilicos.com> wrote: > On windows those need to be double quotes, "*.pep.xml". > > > > -----Original Message----- > From: spctools-discuss@googlegroups.com > > [mailto:spctools-disc...@googlegroups.com] 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 <lmend...@systemsbiology.org> 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 <chrishu...@gmail.com> > 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 <lmend...@systemsbiology.org> 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 < > > > kristian.swearin...@gmail.com>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 <kristian.swearin...@gmail.com> 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" <edeut...@systemsbiology.org> > > > > > > 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: spctools-discuss@googlegroups.com [mailto:spctools- > > > > > > > > disc...@googlegroups.com] On Behalf Of Brian Pratt > > > > > > > > Sent: Tuesday, April 21, 2009 4:11 PM > > > > > > > > To: spctools-discuss@googlegroups.com > > > > > > > > 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: spctools-discuss@googlegroups.com > > > > > > > > [mailto:spctools-disc...@googlegroups.com] 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 > <ntas...@systemsbiology.org> > > > > > 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 > > > > > > > > <vogel....@gmail.com>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 > > > > > > > > <brian.pr...@insilicos.com>wrote: > > > > > > > > > > >> There's not meant to be a limitation - can you give an > > > example > > > > > of a > > > > > > > > > >> command > > > > > > > > > >> line that fails? > > > > > > > > > > >> -----Original Message----- > > > > > > > > > >> From: spctools-discuss@googlegroups.com > > > > > > > > > >> [mailto:spctools-disc...@googlegroups.com] 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. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
