[EMBOSS] question about emma

[Jan T. Kim]

On Tue, Aug 12, 2003 at 08:32:19AM +0300, Henrikki Almusa wrote:
> On Monday 11 August 2003 17:59, Jean Mao wrote:
> > Hi, We just installed emboss and found the default output format of emma is
> > fasta. How can I change the default output to GCG-msf format? Thanks.
> >
> > Jean
> 
> Use option "-osformat msf".
> 
> In http://www.emboss.org there is listing for all options in each program in 
> link applications. Also there is a listing for all possible formats (reports, 
> sequences etc) in user documetation. They might be a good place to find more 
> information.

This is correct, but perhaps not exactly what Jean was looking for. At
least, my understanding of a "default option" is that it takes effect
without being explicitly specified.

I used to achieve this effect by means of aliases, e.g. by putting

    alias emma='emma -osformat msf'

into my ~/.bashrc file, but eventually, my need for such defaults
decreased as I increasingly adopted the habit of putting together shell
scripts that automate the analyses I'm interested in.

However, I've been thinking from time to time that it would sometimes
be handy to have a way to specify defaults for the EMBOSS programs,
e.g. by means of an environment variable or a dotfile. Have I overlooked
this? For example, it might be very convenient at times to change the
default format for sequence output from FASTA to something which
can accomodate more annotation information.

Greetings from Luebeck,
Jan
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