[EMBOSS] Standard Output Flag

[Marko Hyvonen]

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
>
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  _____________________________________

  Marko Hyvonen
  Department of Biochemistry, University of Cambridge
  marko at cryst.bioc.cam.ac.uk
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