[EMBOSS] Antwort: Standard Output Flag

david.bauer at bayer.com david.bauer at bayer.com
Tue Aug 30 06:01:26 UTC 2011

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 
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 
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.


emboss-bounces at 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
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