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