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Questions: ASSEMBLE commandline and FINDPATTERNS

Jan T. Kim a1624091 at athena.rrz.uni-koeln.de
Sat Nov 12 16:19:55 EST 1994

Dear GCG gurus,

I recently switched from using a VMS based GCG installation to using
an OSF/1 based one. Under VMS, I used to create DCL command files that
would call ASSEMBLE to retrieve pieces of sequences surrounding
regions found by FINDPATTERNS. The DCL command sequences looked like:

    $ assemble

Now, under OSF/1, it is not possible pass image data to a program
called from a shell script that easily (it is probably feasible to
have the script create a file with the image data and redirect
ASSEMBLE's stdin to that file, but that seems messy to me). I
tried to specify all parameters in the command line:

    assemble -begin=62 -end=171 -outfile=myseq.mseq myseq.pep

However, ASSEMBLE still asks for the beginning of the segment
interactively. What is wrong?

I'd like to make two remarks:

(1) While messing around with ASSEMBLE, I found that it is possible
to specify any nonsense option witout eliciting any warning or
complaint. Is this normal?

(2) My entire problem would disappear if there was a method to tell
FINDPATTERNS to retrieve sequence segments beginning at some offset
from the first matching symbol and extending for some arbitrary
length for each match found. My current method to achieve this is
a program I wrote which scans a *.find file created by FINDPATTERNS
and produces a DCL command procedure as described above. I ran
into the problem while adapting this hack of mine to generate a
shell script in place of the DCL procedure.

Greetinx & many thanx in advance, Jan
 +- 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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