Rep : how to extend gcg program to work on my personal sequences?

Joao Vasconcelos Costa jcosta at pen.gulbenkian.pt
Thu Jan 18 07:36:56 EST 1996

Mathew Woodwark wrote:
> "FERRAN,edgardo" <Edgardo.FERRAN at TLS1.elfsanofi.fr> (Tel
>\(poste582\)) wrote:
> >Dr. Chyh-Chong Chuang has wrote
> >>
> >> Dear netters:
> >>
> >>      Does some one has the experience to extend gcg program to work on
> >> personal sequences? This is the same to 'create' a personal database,
> >> did any one has done that?
> >>
> >
> >You may 'create' a personal database with the GCG-command dataset. For
> <snip>
> >Edgardo Ferran
> >Sanofi Recherche
> >e-mail: edgardo.ferran at tls1.elfsanofi.fr
> Dataset is a good answer, but here's another suggestion.
> If you don't have too many sequences, or expect to add to your set of sequences on a
> regular basis, I find it easier to keep a file of sequence names up to date. You can
> create this with a directory command and use it like a database. To make a file of
> sequence names (list file) under unix, simply pipe the output of an ls command to a
> file, eg a list file of all the sequences in your directory ending in .seq
> ls *.seq > seq.fil
> and then, to use this with, say, fasta, where you would specify a datalibrary
> (eg: genembl:*), type @seq.fil

Something more if you are using GCG version 8. List files must
start with .. (two periods). Therefore, you should either:
1) edit the file you created as told by Mathew Woodwark
2) start by creating the file seq.fil:
   cat > seq.fil [return]
   .. [return]
   then append the output of ls:
   ls *.seq >> seq.fil

Dr. JOAO V. COSTA                        mailto:jcosta at gulbenkian.pt
Instituto Gulbenkian de Ciencia     Apartado 14, P-2781 Oeiras Codex
PORTUGAL                 phone: +351(1)4435750   fax: +351(1)4435625

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