[EMBOSS] Standard Output Flag

Alen Zamanyan Alen.Zamanyan at loni.ucla.edu
Mon Aug 29 23:49:53 UTC 2011


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.


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