[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
-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-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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