hey joe, many thanks for picking up on this. i will try what you suggested and hope it will help ;-)
many thanks again! cheers, andreas On Thu, Dec 9, 2010 at 12:33 AM, Joe Slagel <[email protected]>wrote: > 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]<spctools-discuss%[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.
