Hello Alen, EMBOSS programs have 2 types of output: text (all programs) and graphics (some programs) You can direct the text output either to a file (-out tmap.res) or to standard output (-stdout) For graphical output you can choose the name of the graphics with -goutfile. The default graphics output is -graph x11 and goes to the X11 terminal. But as far as I know it is not possible to send the graphics to stdandard output. So if you want to post-process the postcript graphics the only choice is to send this to a file and then read from this file.
Cheers, David. emboss-boun...@lists.open-bio.org schrieb am 30/08/2011 01:49:53: > Hello, > > I am trying to run some EMBOSS tools on the command line (without a > prompt). My goal is to have the tools print the output files to > standard output. I noticed that the EMBOSS tools have the -stdout > flag, but I can't seem to get anything printed to standard output. > For instance, I tried the following commands, but to no avail: > > polydot globins.fasta -stdout Yes -auto Yes -graph cps > tmap -stdout Yes -auto Yes opsd.msf -out tmap.res -graph cps > chaos -auto Yes -stdout Yes tembl:j01636 -graph cps > > None of these executions write the results to standard out. Any > ideas as to what I'm doing wrong? I appreciate, in advance, your > time and assistance. > > Thanks, > Alen > > _______________________________________________ > EMBOSS mailing list > EMBOSS@lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss _______________________________________________ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss