EMBOSS default program settings

Peter Rice peter.rice at uk.lionbioscience.com
Fri Nov 8 15:52:05 UTC 2002

Per Johansson wrote:
> I have problems with EMBOSS default program settings in the
> emboss.defaults file.
> set emboss_stdout 1    Works fine, output goes to stdout
> set emboss_verbose 1   Dosen't work

Because help is generated as soon as the -help option is tested.

Changed in the next release to set -verbose before -help.

> set emboss_format embl The programs still outputs fasta format by
> default! And the ONLY sequence format the EMBOSS programs accepts as
> input format is embl!  
> It dosen't work as it should.

Well .... emboss_format sets the default *input* format. You can still say 
fasta::filename to read fasta format

The output format is specified as emboss_outformat

EMBOSS will read all input formats if you only set emboss_outformat

I think you really mean to say:

set emboss_outformat embl

Hope this helps


Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at uk.lionbioscience.com +44 1223 224723

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