Dear Alen,
I believe you should leave out the "Yes", although it might propt for outfile still, but offer stdout as default.
You could also use (in Unix/Linux/etc at least) -outfile /dev/tty to direct the output to terminal.
hth, Marko On Mon, 29 Aug 2011, Alen Zamanyan wrote:
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
_____________________________________ Marko Hyvonen Department of Biochemistry, University of Cambridge ma...@cryst.bioc.cam.ac.uk http://www-cryst.bioc.cam.ac.uk/groups/hyvonen tel: +44-(0)1223-766 044 mobile: +44-(0)7796-174 877 fax: +44-(0)1223-766 002 -------------------------------------- _______________________________________________ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
