I have a batch script which works pretty well, but continuously produces popup consoles while Sequest is running. Does anyone know a possible solution to this? ___________________________________________________________________________ set /p filename= Please, type the name of your .RAW file (excluding the extension): set /p paramfile= Type the name of your parameter file (excluding the extension):
ReAdW -v --mzXML %filename%.RAW runsearch -p%paramfile%.params -P15 %filename%.mzXML sequest -P%paramfile%.params -Dxargs out2XML.exe %filename% 1 -P%paramfile%.params -Etrypsin xinteract -N%filename%.pep.xml -p0.05 -l7 -O %filename%.pep.xml proteinprophet %filename%.pep.xml %filename%.prot.xml _____________________________________________________________________________________ Adjust each line to specify where exactly your files are and save it as a batch script. As I said it works well, but it produces annoying popup as the Sequest search is running. -Ned On Aug 3, 2:38 pm, Joseph Slagel <[email protected]> wrote: > In theory it should work under nmake -- but I won't unleash this on anyone > without extensively testing it first. Hopefully someone else has a > solution, otherwise you could piece together a .bat file pretty easily by > looking at the commands issued in petunia. > > -Joe > > On Wed, Aug 3, 2011 at 11:15 AM, John Bryant <[email protected]>wrote: > > > > > > > > > In Windows 7 > > > On Aug 3, 1:31 pm, Joseph Slagel <[email protected]> > > wrote: > > > Windows or Unix? A long time ago I played around with a Makefile that > > would > > > run the process, and had the added benefit of "knowing" when to rerun > > > certain parts when files changed (such as edits to parameters). > > > > -Joe > > > > On Wed, Aug 3, 2011 at 7:21 AM, John Bryant <[email protected]> > > wrote: > > > > Does anyone have a script that automatically runs the entire TPP > > > > process from converting .RAW files from the mass spectrometer to > > > > identify the proteins using protein prophet? > > > > I have used the TPP for a while and I don't like having to wait for > > > > each step to finish before I manually initiate the next step of the > > > > process. > > > > > -- > > > > 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. -- 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.
