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Questions: ASSEMBLE commandline and FINDPATTERNS

Peter Rice pmr at staffa.sanger.ac.uk
Mon Nov 14 05:16:50 EST 1994


a1624091 at athena.rrz.uni-koeln.de (Jan T. Kim) writes:
>
>    assemble -begin=62 -end=171 -outfile=myseq.mseq myseq.pep
>
>However, ASSEMBLE still asks for the beginning of the segment
>interactively. What is wrong?

The program continues to prompt for a second segment. If you put
-default on the command line the program will stop after the first segment.

>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?

This is normal, and was even the case under VMS because GCG does not
use the standard DCL command line parsing. Of course once you put
-default on the command line the program asks no questions and you
always have to check the output carefully to be sure the command
line was correct.

>(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.

Not to sure what you want here, but perhaps the problem is that FINDPATTERNS
always writes 5 residues before and after the hit. This, for some reason,
is hardcoded into GenApplib:showhits.f

You could work around this by extending the pattern with the required number
of X positions. These will match anything, and will be reported as part of
the hit.

One problem with this approach is that you will miss any hits that do
not have enough flanking residues, but you can catch those by running without
the Xs.

Perhaps a future version will let you specify the extra 5 residues before and
after the hits on the command line - quite easily done by a change to
the showhits function.

------------------------------------------------------------------------
Peter Rice                           | Informatics Division
E-mail: pmr at sanger.ac.uk             | The Sanger Centre
Tel: (44) 1223 494967                | Hinxton Hall, Hinxton,
Fax: (44) 1223 494919                | Cambs, CB10 1RQ
URL: http://www.sanger.ac.uk/~pmr    | England
--
------------------------------------------------------------------------
Peter Rice                           | Informatics Division
E-mail: pmr at sanger.ac.uk             | The Sanger Centre
Tel: (44) 1223 494967                | Hinxton Hall, Hinxton,
Fax: (44) 1223 494919                | Cambs, CB10 1RQ
URL: http://www.sanger.ac.uk/~pmr    | England



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