BTW, in the example where I use "ls *", you may actually need to do a "find . -name '*.pep.xml' -maxdepth 2".
On Wed, Dec 8, 2010 at 2:54 PM, Joe Slagel <[email protected]>wrote: > 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 > -- 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.
