Andreas, There are a couple of options that I can think of depending on exactly what you are trying to do and what data you have but I don't think either of them will get you what you want. I'm sure others have better ideas.
1) You might be able to concat all of the pep.xml files together into a single (or multiple) files using InteractParser (though if the same spectrum appear in more than one file this won't work very well) and then run iprophet on the new file(s). 2) Assuming you are on a linux system, you could try using xargs. Though again this likely will not get you what you want since what xargs does is break up your argument list into (n) groups and execute the command you give it on each group. For example: % echo 1 2 3 4 | xargs -n 2 echo 'args to echo ' args to echo 1 2 args to echo 3 4 Runs the echo on "1 2", then "3 4". The -n 2 flag tells xargs to send 2 arguments per command, without it it will break the arguments up by maximum # of arguments to a command. So something like the following* *might** work for you if only the output file wasn't the last argument, so don't actually try it as it'll overwrite the last pep.xml file in the list: % ls *.pep.xml | xargs InterProphet To get around this restriction, some unix command line foolery could be used: ls *.pep.xml | xargs -n 20 bash -c 'InterProphetParser $0 $* interact.$$.pep.xml' Which should run InterProphetParser (n) times creating (n) interact files. (n) will be defined by the maximum number of arguments/command line size. The '$$' is the process id and is used to avoid overwriting the same interact file. 3) Increase MAX_ARG_PAGES and recompile your kernel. 4) Use a linux kernel version >= 2.6.23, which I understand has variable argument length. http://kernelnewbies.org/Linux_2_6_23#line-84 Besides that -- I'm not sure. -Joe On Tue, Dec 7, 2010 at 5:14 PM, Andreas Quandt <[email protected]>wrote: > dear list, > > i wanted to run iprophet with several 10th of files but do not succeed and > only get an error messages that the argument list is too long. > hence, i was wondering if there is a similar option as for xinteract where > the use of wildcards is possible (e.g. xinteract '*.pep.xml')? > > would be great when someone could help me out and answer on this :-)! > > cheers, > andreas > > -- > 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]<spctools-discuss%[email protected]> > . > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > -- Joe Slagel Institute for Systems Biology [email protected] (206) 732-1362 -- 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.
