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Batch sequence editing?

Jan T. Kim a1624091 at athena.rrz.uni-koeln.de
Wed Aug 3 14:44:07 EST 1994


Dear GCG experts,

do you know of a program in the package that can be used to do a little
non-interactive sequence editing? I would like to extract pieces of
sequences specified by accession number, starting position and length
from the database; and I'd like to automate that with a command procedure.
However, I could not find any program to do the little piece of editing
involved non-interactively. I tried the following command procedure
on VMS to extract the first 5 symbols from muell seq into muell5.seq:

$ seqed muell.seq
:1,5 write muell5.seq
quit

It didn't work, though, seqed reads input from the keyboard rather than
from the script, and after quitting seqed, VMS sees the lines meant for
seqed and ignores them for not beginning with "$".
I checked the online help, the printed manual, and I also checked
rtfm.mit.edu for a FAQ for this group, they didn't have one. Do you
have any idea?
Many thanx in advance for any help.

Kind regards, Jan T. Kim
--
 +- Jan Kim -- X.400:    S=kim;OU=vax;O=mpiz-koeln;P=mpg;A=d400;C=de -+
 |             Internet: kim at vax.mpiz-koeln.mpg.d400.de               |
 |                                                                    |
 *-----=<  hierarchical systems are for files, not for humans  >=-----*



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