Fwd: Re: EMBOSS default program settings

Per Johansson heme at postmark.net
Mon Nov 11 06:32:50 UTC 2002

Thank you Peter,

I DO mean 

set emboss_outformat embl (but I can't find emboss_outformat in the
documentation). When I use 

set emboss_outformat embl 

in the emboss.default file I don't see any effect at all, the default
output format is still fasta, I use emboss-2.4.1 . But I assume this
is not version dependent.


Per Johansson
heme at postmark.net

--- Forwarded Message ---
To: Per Johansson <heme at postmark.net>
Cc: EMBOSS <emboss at embnet.org>
From: Peter Rice <peter.rice at uk.lionbioscience.com>
Subject: Re: EMBOSS default program settings
Date: Fri, 08 Nov 2002 15:52:05 +0000

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

More information about the EMBOSS mailing list