how to specify seq parameters?

[Peter Rice]

Tõnu Margus wrote:

> It is simple question, but I didn't find an answer from documentation.
>  
> How to tell  dotmatcher or whatever an other program in command line, 
> that it will read  sequence in reverse/complement?
> If to run it with an option -sask then it will ask, but from command line?
> Help tells  db:seq1 (Parameter1)    db:seq2 (Parameter2)
> where parameters are optional.

You have many options!!!

To reverse the first sequence:

% dotmatcher db:seq1 -sreverse
% dotmatcher -sreverse1 db:seq1
% dotmatcher -sequencea_sreverse db:seq1
% dotmatcher db:seq1[::r]

Note: -sreverse is an "associated qualifier" (dotmatcher -help -verbose 
lists them). Associated qualifiers, specified as a simple qualifier such as 
'-sreverse', apply to the previous true qualifier, so -sreverse after 
db:seq1 applies only to db:seq1. If you put them at the start of the line, 
they apply to all sequences.

-sreverse1 is the first -sreverse (for the first sequence)
-sequencea_sreverse is the -sreverse for parameter sequencea (the name of 
the first sequence in dotmatcher, see dotmatcher -help for these names)

db:seq1[::r] is an extension to the USA syntax. You can specify -sbegin, 
-send and -sreverse in the USA.

regards,

Peter Rice


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